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<h3 style="margin-top: 20px; margin-bottom: 10px;">

Andreas Tille pushed to branch upstream at <a href="https://salsa.debian.org/med-team/busco">Debian Med / busco</a>

</h3>

<h4 style="margin-top: 10px; margin-bottom: 10px;">

Commits:

</h4>

<ul>

<li>

<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee">d23c473b</a></strong>

<div>

<span> by Andreas Tille </span> <i> at 2023-07-04T11:36:44+02:00 </i>

</div>

<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 5.4.7</pre>

</li>

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<h4 style="margin-top: 10px; margin-bottom: 10px;">

27 changed files:

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<ul>

<li class="file-stats">

<a href="#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">

CHANGELOG

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<li class="file-stats">

<a href="#0398ccd0f49298b10a3d76a47800d2ebecd49859">

LICENSE

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<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

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<li class="file-stats">

<a href="#2e553dba9eac3b861936b9c662ee7d87c706dea0">

bin/busco

</a>

</li>

<li class="file-stats">

<a href="#d0258992426c6db3dfddea46b6a3778071bcad9a">

scripts/generate_plot.py

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<li class="file-stats">

<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">

setup.py

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<li class="file-stats">

<a href="#e497bbf996017c0692c161d2cfed28374276cc73">

src/busco/BuscoConfig.py

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<li class="file-stats">

<a href="#187e8b3b00a66c92055c44aac0cd5c916c6c913e">

src/busco/BuscoDownloadManager.py

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<li class="file-stats">

<a href="#ea2771659c3ac27a7eedddf367d04f0deb13246b">

src/busco/BuscoLogger.py

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<li class="file-stats">

<a href="#414e3994e90f7a52298faa998003b76c548435da">

src/busco/BuscoPlacer.py

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<li class="file-stats">

<a href="#a8fd6f8fc327bd92758f2c1e85bd45f1bad18df0">

src/busco/BuscoRunner.py

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<li class="file-stats">

<a href="#8a51b069da821add214ff0450e58d058e866eb0c">

src/busco/ConfigManager.py

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<li class="file-stats">

<a href="#917b5408af6264ce2b46fc905eaf0095c9aa6bca">

src/busco/__init__.py

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<li class="file-stats">

<a href="#ba1a56246dbcc4652eb6c8edd5d818e5b5c81d88">

src/busco/_version.py

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<a href="#cf0fa70998d90d794d0bbb251526f730829daf8b">

src/busco/analysis/BuscoAnalysis.py

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<li class="file-stats">

<a href="#38e7c7424f4128a85c46ceb416b47ef2236e42b9">

src/busco/analysis/GeneSetAnalysis.py

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<a href="#0750dd8caad8daa319bd078a0d80872708eb7fa7">

src/busco/analysis/GenomeAnalysis.py

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<a href="#ebcdfbf3c61b5f1c742810606673eae398f762bc">

src/busco/analysis/TranscriptomeAnalysis.py

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<a href="#9d54a8efc4f30849596104b53c7b5221e320b1c7">

src/busco/busco_tools/Toolset.py

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<a href="#44a7a9c3d5eacdcf67af9565b069a28d0ef5092d">

src/busco/busco_tools/base.py

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<a href="#a5f82d71f925534007d3cb3b900ad8be00859451">

src/busco/busco_tools/hmmer.py

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<li class="file-stats">

<a href="#53f20ac1df6a610b6a21de977367ddb3704f3394">

src/busco/busco_tools/metaeuk.py

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<a href="#bd0e703ba072ee7447fcc5bd1e634475b3438cf9">

src/busco/run_BUSCO.py

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<li class="file-stats">

<a href="#dba59ea4008347497ea58386e70f0fd75cc9a2e4">

test_data/bacteria/expected_log.txt

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<li class="file-stats">

<a href="#11a346fb4c4f7cb01e1e5466e6712687c54fe746">

test_data/eukaryota/expected_log.txt

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<a href="#ecaba573b4d50cb889221b97937db25cede5aabb">

tests/unittests/AutoLineage_unittests.py

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<li class="file-stats">

<a href="#480430e97df92c2ae922e852fe89a5f357c98cda">

tests/unittests/GenomeAnalysis_unittests.py

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<h4 style="margin-top: 10px; margin-bottom: 10px;">

Changes:

</h4>

<li id="1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a"><strong style="font-weight: bold;">CHANGELOG</strong></a>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1" class="line" lang="plaintext">5.4.7</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2" class="line" lang="plaintext">- Fix bug in overlap handling (Issue #653): this fix also updated the way negative strand coordinates are reported,</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

3

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="plaintext">i.e. <gene_id>:<start>-<stop> instead of <gene_id>:<low>-<high></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

4

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4" class="line" lang="plaintext">- Fix bug in HMMER result filtering (Issue #661)</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

5

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="plaintext">- Fix bug in sequence trimming when exons are removed</span>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

6

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6" class="line" lang="plaintext"></span>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

7

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7" class="line" lang="plaintext">5.4.6</span>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

8

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC8" class="line" lang="plaintext">- Fix mode setting bug in batch mode autolineage (Issue #636)</span>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

9

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="plaintext">- Fix tab discrepancy bug in batch_summary.txt (Issue #643)</span>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

10

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10" class="line" lang="plaintext">- Fix coordinate bug in overlap handling (Issue #644)</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

11

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC11" class="line" lang="plaintext"></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

12

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC12" class="line" lang="plaintext">5.4.5</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

13

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC13" class="line" lang="plaintext">- Fix bug in overlap handling (Issues #627, #633)</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

14

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14" class="line" lang="plaintext">- Fix bug in parasitic check (Issue #594)</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

15

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC15" class="line" lang="plaintext"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1

</td>

<td class="new_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

16

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC16" class="line" lang="plaintext">5.4.4</span>

</pre></td>

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<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

2

</td>

<td class="new_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

17

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC17" class="line" lang="plaintext">- Fix bug in tar option (Issue #591)</span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

3

</td>

<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

18

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC18" class="line" lang="plaintext">- Fix edge case bug in overlap handling (Issue #592)</span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

4

</td>

<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

19

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC19" class="line" lang="plaintext">- Fix overlap adjustment algorithm and trim reported sequences</span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

5

</td>

<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

20

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC20" class="line" lang="plaintext">- Fix file open mode (Issue #622)</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

21

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC21" class="line" lang="plaintext">- Efficiency improvements with more parallel processing</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

6

</td>

<td class="new_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

22

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC22" class="line" lang="plaintext"></span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

7

</td>

<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

23

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC23" class="line" lang="plaintext">5.4.3</span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

8

</td>

<td class="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

24

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC24" class="line" lang="plaintext">- Fix bug in augustus --long pipeline (Issue #586)</span>

</pre></td>

</tr>

</table>

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<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#0398ccd0f49298b10a3d76a47800d2ebecd49859"><strong style="font-weight: bold;">LICENSE</strong></a>

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1

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<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1" class="line" lang="plaintext">The MIT License (MIT)</span>

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<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

2

</td>

<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

2

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="plaintext"></span>

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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

3

</td>

<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext">Copyright (c) 2016-202<span class="idiff left right deletion" style="background-color: #fac5cd;">2</span>, Evgeny Zdobnov (ez@ezlab.org)</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

3

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="plaintext">Copyright (c) 2016-202<span class="idiff left right addition" style="background-color: #c7f0d2;">3</span>, Evgeny Zdobnov (ez@ezlab.org)</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

4

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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="plaintext"></span>

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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

5

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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5" class="line" lang="plaintext">Permission is hereby granted, free of charge, to any person obtaining a copy</span>

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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="plaintext">of this software and associated documentation files (the "Software"), to deal</span>

</pre></td>

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<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong style="font-weight: bold;">README.md</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -43,5 +43,5 @@ BUSCO applications from quality assessments to gene prediction and phylogenomics</td>

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<td class="new_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC43" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC44" class="line" lang="markdown">BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Felipe A. Simão, Robert M. Waterhouse, Panagiotis Ioannidis, Evgenia V. Kriventseva, and Evgeny M. Zdobnov Bioinformatics, published online June 9, 2015 doi: 10.1093/bioinformatics/btv351</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

45

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<td class="new_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC45" class="line" lang="markdown"></span>

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<td class="old_line diff-line-num old" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

46

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<td class="new_line diff-line-num old" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC46" class="line" lang="markdown">Copyright (c) 2016-202<span class="idiff left right deletion" style="background-color: #fac5cd;">2</span>, Evgeny Zdobnov (ez@ezlab.org)</span>

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<td class="old_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC46" class="line" lang="markdown">Copyright (c) 2016-202<span class="idiff left right addition" style="background-color: #c7f0d2;">3</span>, Evgeny Zdobnov (ez@ezlab.org)</span>

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47

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<td class="new_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC47" class="line" lang="markdown">Licensed under the MIT license. See LICENSE.md file.</span></pre></td>

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<li id="2e553dba9eac3b861936b9c662ee7d87c706dea0">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#2e553dba9eac3b861936b9c662ee7d87c706dea0"><strong style="font-weight: bold;">bin/busco</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -2,6 +2,7 @@</td>

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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="python"></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3" class="line" lang="python"></span>

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4

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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

4

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>

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<td class="old_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

5

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="python">    <span class="n" style="color: #333;">__spec__</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

5

</td>

<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

6

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

6

</td>

<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

7

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7" class="line" lang="python">        <span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">busco</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">run_BUSCO</span></span>

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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

7

</td>

<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

8

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">err</span><span class="p">:</span></span>

</pre></td>

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<br>

</li>

<li id="d0258992426c6db3dfddea46b6a3778071bcad9a">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#d0258992426c6db3dfddea46b6a3778071bcad9a"><strong style="font-weight: bold;">scripts/generate_plot.py</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -19,7 +19,7 @@ automatically runs it.</td>

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<td class="old_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

19

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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC19" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

20

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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;">You can find both the resulting R script for customisation and the figure in the working directory.</span></span>

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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

21

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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC21" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

22

</td>

<td class="new_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right deletion" style="background-color: #fac5cd;">2</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right addition" style="background-color: #c7f0d2;">3</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

23

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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC23" class="line" lang="python"><span class="s" style="color: #d14;">Licensed under the MIT license. See LICENSE.md file.</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC24" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC25" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -54,7 +54,7 @@ RCODE = (</td>

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<td class="old_line diff-line-num" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC54" class="line" lang="python">    <span class="s" style="color: #d14;">"# @version 4.0.0</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC55" class="line" lang="python">    <span class="s" style="color: #d14;">"# @since BUSCO 2.0.0</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<td class="new_line diff-line-num" data-linenumber="56" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC56" class="line" lang="python">    <span class="s" style="color: #d14;">"# </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<td class="old_line diff-line-num old" data-linenumber="57" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="57" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC57" class="line" lang="python">    <span class="s" style="color: #d14;">"# Copyright (c) 2016-202<span class="idiff left right deletion" style="background-color: #fac5cd;">2</span>, Evgeny Zdobnov (ez@ezlab.org)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<td class="old_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC57" class="line" lang="python">    <span class="s" style="color: #d14;">"# Copyright (c) 2016-202<span class="idiff left right addition" style="background-color: #c7f0d2;">3</span>, Evgeny Zdobnov (ez@ezlab.org)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<td class="old_line diff-line-num" data-linenumber="58" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="58" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC58" class="line" lang="python">    <span class="s" style="color: #d14;">"# Licensed under the MIT license. See LICENSE.md file.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<td class="new_line diff-line-num" data-linenumber="59" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC59" class="line" lang="python">    <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<td class="new_line diff-line-num" data-linenumber="60" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC60" class="line" lang="python">    <span class="s" style="color: #d14;">"######################################</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<br>

</li>

<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#8e2edce0d507e1297474f25c00cae94258db38d8"><strong style="font-weight: bold;">setup.py</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -4,7 +4,7 @@</td>

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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">.. versionadded:: 3.0.0</span></span>

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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;">.. versionchanged:: 5.0.0</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right deletion" style="background-color: #fac5cd;">2</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right addition" style="background-color: #c7f0d2;">3</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="python"><span class="s" style="color: #d14;">Licensed under the MIT license. See LICENSE.md file.</span></span>

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC9" class="line" lang="python"></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10" class="line" lang="python"><span class="s" style="color: #d14;">This script proceeds to the BUSCO packages installation</span></span>

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<li id="e497bbf996017c0692c161d2cfed28374276cc73">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#e497bbf996017c0692c161d2cfed28374276cc73"><strong style="font-weight: bold;">src/busco/BuscoConfig.py</strong></a>

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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -206,31 +206,31 @@ class BaseConfig(ConfigParser, metaclass=ABCMeta):</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC206" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">update_mode</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>

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<td class="new_line diff-line-num" data-linenumber="207" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC207" class="line" lang="python">        <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mode"</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="208" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="208" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC208" class="line" lang="python">        <span class="n" style="color: #333;">domain</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"domain"</span><span class="p">)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="209" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="209" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC209" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">mode</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">==</span></span><span class="idiff right deletion" style="background-color: #fac5cd;"> </span><span class="s" style="color: #d14;">"genome"</span><span class="p">:</span></span>

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<td class="old_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="209" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC209" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"genome"</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="ow" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">in</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff right addition" style="background-color: #c7f0d2;">mode</span></span><span class="p">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="210" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="210" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC210" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">domain</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"prokaryota"</span><span class="p">,</span> <span class="s" style="color: #d14;">"viruses"</span><span class="p">]:</span></span>

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<td class="old_line diff-line-num old" data-linenumber="211" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="211" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC211" class="line" lang="python">                <span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">self</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">set</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">(</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"busco_run"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"</span>mode<span class="idiff deletion" style="background-color: #fac5cd;">"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span> <span class="s" style="color: #d14;">"prok_genome"</span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">)</span></span></span>

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<td class="old_line diff-line-num new" data-linenumber="212" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="211" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC211" class="line" lang="python">                <span class="n" style="color: #333;">mode</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right addition" style="background-color: #c7f0d2;">=</span></span> <span class="s" style="color: #d14;">"prok_genome"</span></span>

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<td class="old_line diff-line-num" data-linenumber="212" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="212" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC212" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">domain</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"eukaryota"</span><span class="p">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="213" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="213" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC213" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">getboolean</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"use_augustus"</span><span class="p">):</span></span>

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<td class="new_line diff-line-num old" data-linenumber="214" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC214" class="line" lang="python">                    <span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">self</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">set</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">(</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"busco_run"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"</span>mode<span class="idiff deletion" style="background-color: #fac5cd;">"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span> <span class="s" style="color: #d14;">"euk_genome_aug"</span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">)</span></span></span>

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<td class="old_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="214" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

214

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC214" class="line" lang="python">                    <span class="n" style="color: #333;">mode</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right addition" style="background-color: #c7f0d2;">=</span></span> <span class="s" style="color: #d14;">"euk_genome_aug"</span></span>

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<td class="old_line diff-line-num" data-linenumber="215" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

215

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<td class="new_line diff-line-num" data-linenumber="215" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC215" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="old_line diff-line-num old" data-linenumber="216" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

216

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<td class="new_line diff-line-num old" data-linenumber="216" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC216" class="line" lang="python">                    <span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">self</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">set</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">(</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"busco_run"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"</span>mode<span class="idiff deletion" style="background-color: #fac5cd;">"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span> <span class="s" style="color: #d14;">"euk_genome_met"</span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">)</span></span></span>

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<td class="old_line diff-line-num new" data-linenumber="217" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="216" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

216

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC216" class="line" lang="python">                    <span class="n" style="color: #333;">mode</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right addition" style="background-color: #c7f0d2;">=</span></span> <span class="s" style="color: #d14;">"euk_genome_met"</span></span>

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<td class="old_line diff-line-num" data-linenumber="217" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

217

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<td class="new_line diff-line-num" data-linenumber="217" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC217" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="old_line diff-line-num old" data-linenumber="218" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

218

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<td class="new_line diff-line-num old" data-linenumber="218" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC218" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="nc" style="color: #458; font-weight: 600;">BatchFatalError</span><span class="p">(</span></span>

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<td class="old_line diff-line-num old" data-linenumber="219" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

219

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<td class="new_line diff-line-num old" data-linenumber="218" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC219" class="line" lang="python">                    <span class="s" style="color: #d14;">"Unrecognized mode {}"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mode"</span><span class="p">))</span></span>

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<td class="old_line diff-line-num old" data-linenumber="220" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

220

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<td class="new_line diff-line-num old" data-linenumber="218" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC220" class="line" lang="python">                <span class="p">)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="221" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC218" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="nc" style="color: #458; font-weight: 600;">BatchFatalError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unrecognized mode {}"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">mode</span><span class="p">))</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="221" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="219" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC219" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="222" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

222

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<td class="new_line diff-line-num" data-linenumber="220" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC220" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"transcriptome"</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="223" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="221" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC221" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">domain</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"prokaryota"</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="224" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="222" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC224" class="line" lang="python">                <span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">self</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">set</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">(</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"busco_run"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"</span>mode<span class="idiff deletion" style="background-color: #fac5cd;">"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span> <span class="s" style="color: #d14;">"prok_tran"</span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">)</span></span></span>

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<td class="old_line diff-line-num new" data-linenumber="225" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="222" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

222

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC222" class="line" lang="python">                <span class="n" style="color: #333;">mode</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right addition" style="background-color: #c7f0d2;">=</span></span> <span class="s" style="color: #d14;">"prok_tran"</span></span>

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<td class="old_line diff-line-num" data-linenumber="225" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

225

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<td class="new_line diff-line-num" data-linenumber="223" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC223" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">domain</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"eukaryota"</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="226" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

226

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<td class="new_line diff-line-num old" data-linenumber="224" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC226" class="line" lang="python">                <span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">self</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">set</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">(</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"busco_run"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"</span>mode<span class="idiff deletion" style="background-color: #fac5cd;">"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span> <span class="s" style="color: #d14;">"euk_tran"</span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">)</span></span></span>

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<td class="old_line diff-line-num new" data-linenumber="227" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="224" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

224

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC224" class="line" lang="python">                <span class="n" style="color: #333;">mode</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff right addition" style="background-color: #c7f0d2;">=</span></span> <span class="s" style="color: #d14;">"euk_tran"</span></span>

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<td class="old_line diff-line-num" data-linenumber="227" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

227

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<td class="new_line diff-line-num" data-linenumber="225" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC225" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">domain</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"viruses"</span><span class="p">:</span></span>

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<td class="old_line diff-line-num old" data-linenumber="228" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="226" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC228" class="line" lang="python">                <span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">self</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">set</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">(</span></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="229" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

229

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<td class="new_line diff-line-num old" data-linenumber="226" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC229" class="line" lang="python">                <span class="idiff left deletion" style="background-color: #fac5cd;">    </span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"busco_run"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"mode"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="s" style="color: #d14;"><span class="idiff right deletion" style="background-color: #fac5cd;">"prok_genome"</span></span></span>

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<td class="old_line diff-line-num old" data-linenumber="230" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

230

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<td class="new_line diff-line-num old" data-linenumber="226" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC230" class="line" lang="python"><span class="idiff left deletion" style="background-color: #fac5cd;">                </span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">)</span></span><span class="idiff deletion" style="background-color: #fac5cd;">  </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right deletion" style="background-color: #fac5cd;"># Suggested by Mose - Prodigal may perform better on viruses than BLAST + HMMER.</span></span></span>

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<td class="old_line diff-line-num new" data-linenumber="231" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="226" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC226" class="line" lang="python">                <span class="n" style="color: #333;"><span class="idiff left addition" style="background-color: #c7f0d2;">mode</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"prok_genome"</span></span><span class="idiff addition" style="background-color: #c7f0d2;">  </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition" style="background-color: #c7f0d2;"># Suggested by Mose - Prodigal may perform better on viruses</span></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="231" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC227" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition" style="background-color: #c7f0d2;"># than BLAST + HMMER.</span></span></span>

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<td class="old_line diff-line-num new" data-linenumber="231" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC228" class="line" lang="python"></span>

</pre></td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC229" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC230" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="nc" style="color: #458; font-weight: 600;">BatchFatalError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unrecognized mode {}"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">mode</span><span class="p">))</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC231" class="line" lang="python"></span>

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<td class="old_line diff-line-num new" data-linenumber="234" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC232" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mode</span><span class="p">,</span> <span class="n" style="color: #333;">domain</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC233" class="line" lang="python"></span>

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<td class="new_line diff-line-num" data-linenumber="234" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC234" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_mode_specific_parameters</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>

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<td class="new_line diff-line-num" data-linenumber="235" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC235" class="line" lang="python">        <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mode"</span><span class="p">)</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC236" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"euk_genome_aug"</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="283" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="283" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -283,7 +283,9 @@ class BaseConfig(ConfigParser, metaclass=ABCMeta):</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC283" class="line" lang="python">                    <span class="s" style="color: #d14;">"domain"</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC284" class="line" lang="python">                <span class="p">]</span>  <span class="c1" style="color: #998; font-style: italic;"># Necessary to set domain kw first to enable augustus and prodigal arguments to be handled properly</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC285" class="line" lang="python">                <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">set</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"domain"</span><span class="p">,</span> <span class="n" style="color: #333;">domain</span><span class="p">)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="286" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="286" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC286" class="line" lang="python">                <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">update_mode</span><span class="p">()</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC286" class="line" lang="python">                <span class="n" style="color: #333;">mode</span><span class="p">,</span> <span class="n" style="color: #333;">domain</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">update_mode</span><span class="p">()</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC287" class="line" lang="python">                <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">set</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mode"</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="288" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC288" class="line" lang="python">                <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">set</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"domain"</span><span class="p">,</span> <span class="n" style="color: #333;">domain</span><span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="289" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC289" class="line" lang="python">                <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">dataset_kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"domain"</span><span class="p">]</span></span>

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<td class="new_line diff-line-num" data-linenumber="290" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC290" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dataset_kwargs</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">items</span><span class="p">():</span></span>

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<td class="new_line diff-line-num" data-linenumber="291" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC291" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"species"</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="316" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="318" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -316,7 +318,7 @@ class BaseConfig(ConfigParser, metaclass=ABCMeta):</td>

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<td class="new_line diff-line-num" data-linenumber="318" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC318" class="line" lang="python">                    <span class="p">]:</span></span>

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<td class="new_line diff-line-num" data-linenumber="319" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC319" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mode"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span></span>

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<td class="new_line diff-line-num" data-linenumber="320" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC320" class="line" lang="python">                            <span class="s" style="color: #d14;">"euk_genome_met"</span><span class="p">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="319" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="321" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC319" class="line" lang="python">                            <span class="s" style="color: #d14;">"euk_tran"</span><span class="p"><span class="idiff left right deletion" style="background-color: #fac5cd;">,</span></span></span>

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<td class="new_line diff-line-num new" data-linenumber="321" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC321" class="line" lang="python">                            <span class="s" style="color: #d14;">"euk_tran"</span></span>

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<td class="new_line diff-line-num" data-linenumber="322" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC322" class="line" lang="python">                        <span class="p">]:</span></span>

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<td class="old_line diff-line-num" data-linenumber="321" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="323" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC323" class="line" lang="python">                            <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">set</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="324" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC324" class="line" lang="python">                    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="336" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="338" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -336,6 +338,18 @@ class BaseConfig(ConfigParser, metaclass=ABCMeta):</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC338" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">exists</span><span class="p">(</span><span class="n" style="color: #333;">main_out</span><span class="p">):</span></span>

</pre></td>

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<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="337" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

337

</td>

<td class="new_line diff-line-num" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

339

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC339" class="line" lang="python">            <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">makedirs</span><span class="p">(</span><span class="n" style="color: #333;">main_out</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="338" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

338

</td>

<td class="new_line diff-line-num" data-linenumber="340" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

340

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC340" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="341" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

341

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC341" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">reset</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="342" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

342

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC342" class="line" lang="python">        <span class="n" style="color: #333;">options_to_reset</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"domain_run_name"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ambiguous_cd_range_lower"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ambiguous_cd_range_upper"</span><span class="p">,</span> <span class="s" style="color: #d14;">"creation_date"</span><span class="p">,</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="343" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

343

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC343" class="line" lang="python">                            <span class="s" style="color: #d14;">"domain"</span><span class="p">,</span> <span class="s" style="color: #d14;">"in"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lineage_results_dir"</span><span class="p">,</span> <span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="s" style="color: #d14;">"number_of_buscos"</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

344

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC344" class="line" lang="python">                            <span class="s" style="color: #d14;">"number_of_species"</span><span class="p">,</span> <span class="s" style="color: #d14;">"main_out"</span><span class="p">,</span> <span class="s" style="color: #d14;">"prodigal_genetic_code"</span><span class="p">]</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="345" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

345

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC345" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">option</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">options_to_reset</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="346" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

346

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC346" class="line" lang="python">            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="347" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

347

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC347" class="line" lang="python">                <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">remove_option</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="n" style="color: #333;">option</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="348" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

348

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC348" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">NoOptionError</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="349" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

349

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC349" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="350" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

350

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC350" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">getboolean</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"auto-lineage"</span><span class="p">):</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="351" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

351

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC351" class="line" lang="python">            <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">remove_option</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lineage_dataset"</span><span class="p">)</span></span>

</pre></td>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC352" class="line" lang="python"></span>

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339

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<td class="new_line diff-line-num" data-linenumber="353" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC353" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_results_dirname</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">lineage</span><span class="p">):</span></span>

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340

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<td class="new_line diff-line-num" data-linenumber="354" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC354" class="line" lang="python">        <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">set</span><span class="p">(</span></span>

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341

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<td class="new_line diff-line-num" data-linenumber="355" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC355" class="line" lang="python">            <span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="653" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -653,7 +667,9 @@ class BuscoConfigMain(BaseConfig):</td>

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653

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<td class="new_line diff-line-num" data-linenumber="667" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

667

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC667" class="line" lang="python">                    <span class="p">):</span></span>

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<td class="old_line diff-line-num" data-linenumber="654" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

654

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<td class="new_line diff-line-num" data-linenumber="668" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

668

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC668" class="line" lang="python">                        <span class="k" style="font-weight: 600;">raise</span> <span class="nc" style="color: #458; font-weight: 600;">BatchFatalError</span><span class="p">(</span></span>

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655

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<td class="new_line diff-line-num" data-linenumber="669" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

669

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC669" class="line" lang="python">                            <span class="s" style="color: #d14;">"Unknown mode {}.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'Mode' parameter must be one of "</span></span>

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<td class="old_line diff-line-num old" data-linenumber="656" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

656

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<td class="new_line diff-line-num old" data-linenumber="670" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC656" class="line" lang="python">                            <span class="s" style="color: #d14;">"['genome', 'transcriptome', 'proteins']"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="670" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

670

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC670" class="line" lang="python">                            <span class="s" style="color: #d14;">"['genome', 'transcriptome', 'proteins']"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>

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<td class="old_line diff-line-num new" data-linenumber="657" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="671" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

671

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC671" class="line" lang="python">                                <span class="n" style="color: #333;">value</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC672" class="line" lang="python">                            <span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="673" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC673" class="line" lang="python">                        <span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="658" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

658

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<td class="new_line diff-line-num" data-linenumber="674" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC674" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">synonyms</span><span class="p">[</span><span class="s" style="color: #d14;">"genome"</span><span class="p">]:</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="659" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

659

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<td class="new_line diff-line-num" data-linenumber="675" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

675

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC675" class="line" lang="python">                        <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">set</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mode"</span><span class="p">,</span> <span class="s" style="color: #d14;">"genome"</span><span class="p">)</span></span>

</pre></td>

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<br>

</li>

<li id="187e8b3b00a66c92055c44aac0cd5c916c6c913e">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#187e8b3b00a66c92055c44aac0cd5c916c6c913e"><strong style="font-weight: bold;">src/busco/BuscoDownloadManager.py</strong></a>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;">.. versionadded:: 4.0.0</span></span>

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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">.. versionchanged:: 5.4.0</span></span>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right deletion" style="background-color: #fac5cd;">2</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right addition" style="background-color: #c7f0d2;">3</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10" class="line" lang="python"><span class="s" style="color: #d14;">Licensed under the MIT license. See LICENSE.md file.</span></span>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC11" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

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<br>

</li>

<li id="ea2771659c3ac27a7eedddf367d04f0deb13246b">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#ea2771659c3ac27a7eedddf367d04f0deb13246b"><strong style="font-weight: bold;">src/busco/BuscoLogger.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -8,7 +8,7 @@</td>

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">This is a logger for the pipeline that extends the default Python logger class</span></span>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

11

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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC11" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right deletion" style="background-color: #fac5cd;">2</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

11

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC11" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right addition" style="background-color: #c7f0d2;">3</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

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12

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;">Licensed under the MIT license. See LICENSE.md file.</span></span>

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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

13

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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC13" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

14

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

</pre></td>

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<br>

</li>

<li id="414e3994e90f7a52298faa998003b76c548435da">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#414e3994e90f7a52298faa998003b76c548435da"><strong style="font-weight: bold;">src/busco/BuscoPlacer.py</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -8,7 +8,7 @@</td>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="python"><span class="s" style="color: #d14;">.. versionadded:: 4.0.0</span></span>

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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">.. versionchanged:: 5.4.0</span></span>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

11

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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC11" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right deletion" style="background-color: #fac5cd;">2</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC11" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right addition" style="background-color: #c7f0d2;">3</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

12

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

12

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;">Licensed under the MIT license. See LICENSE.md file.</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

13

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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC13" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

</pre></td>

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<br>

</li>

<li id="a8fd6f8fc327bd92758f2c1e85bd45f1bad18df0">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#a8fd6f8fc327bd92758f2c1e85bd45f1bad18df0"><strong style="font-weight: bold;">src/busco/BuscoRunner.py</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="107" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="107" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -107,6 +107,7 @@ class SingleRunner:</td>

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<td class="new_line diff-line-num" data-linenumber="107" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC107" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">reset</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>

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<td class="old_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC108" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">runner</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nf" style="color: #900; font-weight: 600;">type</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">).</span><span class="n" style="color: #333;">all_runners</span><span class="p">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="109" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="109" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC109" class="line" lang="python">            <span class="n" style="color: #333;">runner</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">reset</span><span class="p">()</span></span>

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<td class="new_line diff-line-num" data-linenumber="111" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC111" class="line" lang="python">            <span class="n" style="color: #333;">runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">reset</span><span class="p">()</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC112" class="line" lang="python">        <span class="nf" style="color: #900; font-weight: 600;">type</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">).</span><span class="n" style="color: #333;">all_runners</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">set</span><span class="p">()</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC113" class="line" lang="python"></span>

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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -160,9 +161,14 @@ class SingleRunner:</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC161" class="line" lang="python"></span>

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<td class="new_line diff-line-num" data-linenumber="162" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC162" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">getboolean</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"tar"</span><span class="p">):</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC163" class="line" lang="python">                <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">compress_folders</span><span class="p">()</span></span>

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<td class="new_line diff-line-num old" data-linenumber="164" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC163" class="line" lang="python">            <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">compile_summary</span><span class="p">()</span></span>

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<td class="old_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC164" class="line" lang="python">            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<td class="old_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC165" class="line" lang="python">                <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">compile_summary</span><span class="p">()</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC166" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>

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<td class="new_line diff-line-num new" data-linenumber="167" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC167" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="nc" style="color: #458; font-weight: 600;">BatchFatalError</span><span class="p">(</span></span>

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<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC168" class="line" lang="python">                    <span class="s" style="color: #d14;">"BUSCO encountered a problem. This is possibly caused by restarting a previously completed run with different parameters."</span><span class="p">)</span></span>

</pre></td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC169" class="line" lang="python">            <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">runner</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">finish</span><span class="p">(</span><span class="n" style="color: #333;">time</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">time</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">start_time</span><span class="p">)</span></span>

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165

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC170" class="line" lang="python"></span>

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<td class="old_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC171" class="line" lang="python"></span>

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166

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<td class="new_line diff-line-num" data-linenumber="172" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC172" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">BuscoError</span><span class="p">:</span></span>

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<td class="new_line diff-line-num" data-linenumber="173" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC173" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">runner</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="168" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="174" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC174" class="line" lang="python">                <span class="nf" style="color: #900; font-weight: 600;">type</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">).</span><span class="n" style="color: #333;">all_runners</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">add</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">runner</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="268" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="274" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -268,14 +274,14 @@ class BatchRunner:</td>

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<td class="new_line diff-line-num" data-linenumber="274" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC274" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">BuscoError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">be</span><span class="p">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="269" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="275" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC275" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"did not recognize any genes"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">be</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="270" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="276" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC276" class="line" lang="python">                    <span class="nf" style="color: #900; font-weight: 600;">type</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">).</span><span class="n" style="color: #333;">batch_results</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span></span>

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<td class="old_line diff-line-num old" data-linenumber="271" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="277" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC271" class="line" lang="python">                        <span class="s" style="color: #d14;">"{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">No genes found</span><span class="se" style="color: #d14;">\t\t\t\t\t\t\t\t\t\t<span class="idiff left right deletion" style="background-color: #fac5cd;">\t\t\t</span>\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>

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<td class="old_line diff-line-num old" data-linenumber="272" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="277" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC272" class="line" lang="python">                            <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">basename</span><span class="p">(</span><span class="n" style="color: #333;">input_file</span><span class="p">)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="273" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="277" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC277" class="line" lang="python">                        <span class="s" style="color: #d14;">"{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">No genes found</span><span class="se" style="color: #d14;">\t\t\t\t\t\t\t\t\t\t</span><span class="s" style="color: #d14;"><span class="idiff left right addition" style="background-color: #c7f0d2;">{}</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>

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<td class="old_line diff-line-num new" data-linenumber="273" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="278" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC278" class="line" lang="python">                            <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">basename</span><span class="p">(</span><span class="n" style="color: #333;">input_file</span><span class="p">)<span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"</span></span><span class="se" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">\t\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">*</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">int</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">single_run</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">config</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">getboolean</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"busco_run"</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"auto-lineage"</span></span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">))</span></span></span>

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<td class="new_line diff-line-num" data-linenumber="279" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC279" class="line" lang="python">                        <span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="274" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="280" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC280" class="line" lang="python">                    <span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="275" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="281" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC281" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="new_line diff-line-num" data-linenumber="282" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC282" class="line" lang="python">                    <span class="nf" style="color: #900; font-weight: 600;">type</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">).</span><span class="n" style="color: #333;">batch_results</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span></span>

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<td class="old_line diff-line-num old" data-linenumber="277" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="283" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC277" class="line" lang="python">                        <span class="s" style="color: #d14;">"{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Run failed; check logs</span><span class="se" style="color: #d14;">\t\t\t\t\t\t\t\t\t\t<span class="idiff left right deletion" style="background-color: #fac5cd;">\t\t\t</span>\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>

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<td class="old_line diff-line-num old" data-linenumber="278" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="283" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC278" class="line" lang="python">                            <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">basename</span><span class="p">(</span><span class="n" style="color: #333;">input_file</span><span class="p">)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="279" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="283" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC283" class="line" lang="python">                        <span class="s" style="color: #d14;">"{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Run failed; check logs</span><span class="se" style="color: #d14;">\t\t\t\t\t\t\t\t\t\t</span><span class="s" style="color: #d14;"><span class="idiff left right addition" style="background-color: #c7f0d2;">{}</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>

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<td class="old_line diff-line-num new" data-linenumber="279" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="284" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC284" class="line" lang="python">                            <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">basename</span><span class="p">(</span><span class="n" style="color: #333;">input_file</span><span class="p">)<span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"</span></span><span class="se" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">\t\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">*</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">int</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">single_run</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">config</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">getboolean</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"busco_run"</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"auto-lineage"</span></span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">))</span></span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC285" class="line" lang="python">                        <span class="p">)</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC286" class="line" lang="python">                    <span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="345" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -345,33 +351,11 @@ class AnalysisRunner:</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC351" class="line" lang="python">        <span class="nf" style="color: #900; font-weight: 600;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">BuscoAnalysis</span><span class="p">,</span> <span class="s" style="color: #d14;">"config"</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">)</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC352" class="line" lang="python"></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC353" class="line" lang="python">        <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">input_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"in"</span><span class="p">)</span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC348" class="line" lang="python">        <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mode"</span><span class="p">)</span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC349" class="line" lang="python">        <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">domain</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"domain"</span><span class="p">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="354" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC354" class="line" lang="python">        <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span><span class="p">,</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">domain</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">update_mode</span><span class="p">()</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC355" class="line" lang="python">        <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">lineage_basename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">basename</span><span class="p">(</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC356" class="line" lang="python">            <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lineage_dataset"</span><span class="p">)</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC357" class="line" lang="python">        <span class="p">)</span></span>

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<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC354" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"genome"</span><span class="p">:</span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC355" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">domain</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"prokaryota"</span><span class="p">,</span> <span class="s" style="color: #d14;">"viruses"</span><span class="p">]:</span></span>

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<td class="old_line diff-line-num old" data-linenumber="356" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

356

</td>

<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC356" class="line" lang="python">                <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"prok_genome"</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="357" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

357

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<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC357" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">domain</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"eukaryota"</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="358" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

358

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<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC358" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">getboolean</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"use_augustus"</span><span class="p">):</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

359

</td>

<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC359" class="line" lang="python">                    <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"euk_genome_aug"</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="360" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

360

</td>

<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC360" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="361" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

361

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<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC361" class="line" lang="python">                    <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"euk_genome_met"</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="362" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

362

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<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC362" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="363" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

363

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<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC363" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="nc" style="color: #458; font-weight: 600;">BatchFatalError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unrecognized mode {}"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span><span class="p">))</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="364" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

364

</td>

<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC364" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="365" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

365

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<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC365" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"transcriptome"</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="366" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

366

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<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC366" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">domain</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"prokaryota"</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="367" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

367

</td>

<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC367" class="line" lang="python">                <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"prok_tran"</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="368" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

368

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<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC368" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">domain</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"eukaryota"</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="369" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

369

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<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC369" class="line" lang="python">                <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"euk_tran"</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="370" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

370

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<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC370" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">domain</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"viruses"</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="371" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

371

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<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC371" class="line" lang="python">                <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"prok_genome"</span>  <span class="c1" style="color: #998; font-style: italic;"># Suggested by Mose - Prodigal may perform better on viruses</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="372" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

372

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<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC372" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># than BLAST + HMMER.</span></span>

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<td class="old_line diff-line-num old" data-linenumber="373" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

373

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<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC373" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="old_line diff-line-num old" data-linenumber="374" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

374

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<td class="new_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC374" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="nc" style="color: #458; font-weight: 600;">BatchFatalError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unrecognized mode {}"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span><span class="p">))</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="375" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

375

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<td class="new_line diff-line-num" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC359" class="line" lang="python">        <span class="n" style="color: #333;">analysis_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">type</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">).</span><span class="n" style="color: #333;">mode_dict</span><span class="p">[</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="376" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="360" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC360" class="line" lang="python">        <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">analysis_type</span><span class="p">()</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="377" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

377

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<td class="new_line diff-line-num" data-linenumber="361" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC361" class="line" lang="python">        <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">summary</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="759" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="743" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -759,7 +743,7 @@ class AnalysisRunner:</td>

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<td class="old_line diff-line-num" data-linenumber="759" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

759

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<td class="new_line diff-line-num" data-linenumber="743" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

743

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC743" class="line" lang="python">                        <span class="n" style="color: #333;">auto_lineage_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Consider using the auto-lineage mode to select a more specific lineage."</span></span>

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<td class="old_line diff-line-num" data-linenumber="760" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

760

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<td class="new_line diff-line-num" data-linenumber="744" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

744

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC744" class="line" lang="python">                        <span class="n" style="color: #333;">final_output_results</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">auto_lineage_line</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="761" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

761

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<td class="new_line diff-line-num" data-linenumber="745" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

745

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC745" class="line" lang="python">                    <span class="k" style="font-weight: 600;">with</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span></span>

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<td class="old_line diff-line-num old" data-linenumber="762" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

762

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<td class="new_line diff-line-num old" data-linenumber="746" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC762" class="line" lang="python">                        <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">analysis</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">hmmer_runner</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">.</span></span><span class="n" style="color: #333;">short_summary_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"a"</span></span>

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<td class="old_line diff-line-num new" data-linenumber="763" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="746" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

746

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC746" class="line" lang="python">                        <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">short_summary_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"a"</span></span>

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<td class="old_line diff-line-num" data-linenumber="763" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

763

</td>

<td class="new_line diff-line-num" data-linenumber="747" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

747

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC747" class="line" lang="python">                    <span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">short_summary_file</span><span class="p">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="764" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

764

</td>

<td class="new_line diff-line-num" data-linenumber="748" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

748

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC748" class="line" lang="python">                        <span class="n" style="color: #333;">short_summary_file</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="n" style="color: #333;">positive_parasitic_line</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="765" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

765

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<td class="new_line diff-line-num" data-linenumber="749" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

749

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC749" class="line" lang="python"></span>

</pre></td>

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<br>

</li>

<li id="8a51b069da821add214ff0450e58d058e866eb0c">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#8a51b069da821add214ff0450e58d058e866eb0c"><strong style="font-weight: bold;">src/busco/ConfigManager.py</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -6,7 +6,7 @@</td>

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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

6

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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

6

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;">.. versionadded:: 3.0.0</span></span>

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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

7

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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

7

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">.. versionchanged:: 5.4.0</span></span>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

8

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

8

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

9

</td>

<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right deletion" style="background-color: #fac5cd;">2</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

9

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right addition" style="background-color: #c7f0d2;">3</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

10

</td>

<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

10

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10" class="line" lang="python"><span class="s" style="color: #d14;">Licensed under the MIT license. See LICENSE.md file.</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

11

</td>

<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

11

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC11" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

12

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

12

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

</pre></td>

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<br>

</li>

<li id="917b5408af6264ce2b46fc905eaf0095c9aa6bca">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#917b5408af6264ce2b46fc905eaf0095c9aa6bca"><strong style="font-weight: bold;">src/busco/__init__.py</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -5,7 +5,7 @@</td>

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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

5

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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;">   :synopsis: BUSCO - Benchmarking Universal Single-Copy Orthologs.</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

6

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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

6

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="python"></span>

</pre></td>

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<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

7

</td>

<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

7

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7" class="line" lang="python"></span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

8

</td>

<td class="new_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC8" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right deletion" style="background-color: #fac5cd;">2</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

8

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC8" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right addition" style="background-color: #c7f0d2;">3</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

9

</td>

<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

9

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">Licensed under the MIT license. See LICENSE.md file.</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

10

</td>

<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

10

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

11

</td>

<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

11

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC11" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

</pre></td>

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</table>

<br>

</li>

<li id="ba1a56246dbcc4652eb6c8edd5d818e5b5c81d88">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#ba1a56246dbcc4652eb6c8edd5d818e5b5c81d88"><strong style="font-weight: bold;">src/busco/_version.py</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -2,8 +2,8 @@</td>

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<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

2

</td>

<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># coding: utf-8</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

3

</td>

<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

3

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

</pre></td>

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<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

4

</td>

<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

4

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="python"></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

5

</td>

<td class="new_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right deletion" style="background-color: #fac5cd;">2</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

5

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right addition" style="background-color: #c7f0d2;">3</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

6

</td>

<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

6

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;">Licensed under the MIT license. See LICENSE.md file.</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

7

</td>

<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

7

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

8

</td>

<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

8

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

9

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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"5.4.<span class="idiff left right deletion" style="background-color: #fac5cd;">4</span>"</span></span></pre></td>

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

9

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"5.4.<span class="idiff left right addition" style="background-color: #c7f0d2;">7</span>"</span></span></pre></td>

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<br>

</li>

<li id="cf0fa70998d90d794d0bbb251526f730829daf8b">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#cf0fa70998d90d794d0bbb251526f730829daf8b"><strong style="font-weight: bold;">src/busco/analysis/BuscoAnalysis.py</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -6,7 +6,7 @@</td>

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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;">.. versionadded:: 3.0.0</span></span>

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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">.. versionchanged:: 5.4.0</span></span>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right deletion" style="background-color: #fac5cd;">2</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right addition" style="background-color: #c7f0d2;">3</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10" class="line" lang="python"><span class="s" style="color: #d14;">Licensed under the MIT license. See LICENSE.md file.</span></span>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC11" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC12" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="154" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="154" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -154,7 +154,6 @@ class BuscoAnalysis(metaclass=ABCMeta):</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC154" class="line" lang="python"></span>

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<td class="new_line diff-line-num" data-linenumber="155" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC155" class="line" lang="python"><span class="s" style="color: #d14;">        :raises BuscoError: if the dataset is missing files or folders</span></span>

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<td class="old_line diff-line-num" data-linenumber="156" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC156" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<td class="new_line diff-line-num old" data-linenumber="157" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC157" class="line" lang="python"></span>

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157

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC157" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Check hmm files exist</span></span>

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<td class="old_line diff-line-num" data-linenumber="159" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

159

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<td class="new_line diff-line-num" data-linenumber="158" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

158

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC158" class="line" lang="python">        <span class="n" style="color: #333;">files</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">listdir</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">lineage_dataset</span><span class="p">,</span> <span class="s" style="color: #d14;">"hmms"</span><span class="p">))</span></span>

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<td class="old_line diff-line-num" data-linenumber="160" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

160

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<td class="new_line diff-line-num" data-linenumber="159" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

159

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC159" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">files</span><span class="p">:</span></span>

</pre></td>

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<br>

</li>

<li id="38e7c7424f4128a85c46ceb416b47ef2236e42b9">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#38e7c7424f4128a85c46ceb416b47ef2236e42b9"><strong style="font-weight: bold;">src/busco/analysis/GeneSetAnalysis.py</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -6,7 +6,7 @@</td>

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6

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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

6

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;">.. versionadded:: 3.0.0</span></span>

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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

7

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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

7

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">.. versionchanged:: 5.4.0</span></span>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

8

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

9

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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right deletion" style="background-color: #fac5cd;">2</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right addition" style="background-color: #c7f0d2;">3</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10" class="line" lang="python"><span class="s" style="color: #d14;">Licensed under the MIT license. See LICENSE.md file.</span></span>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

11

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC11" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

</pre></td>

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<br>

</li>

<li id="0750dd8caad8daa319bd078a0d80872708eb7fa7">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#0750dd8caad8daa319bd078a0d80872708eb7fa7"><strong style="font-weight: bold;">src/busco/analysis/GenomeAnalysis.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -4,9 +4,9 @@</td>

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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">.. module:: GenomeAnalysis</span></span>

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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;">   :synopsis: GenomeAnalysis implements genome analysis specifics</span></span>

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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

6

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;">.. versionadded:: 3.0.0</span></span>

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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

7

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<td class="new_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">.. versionchanged:: 5.4.<span class="idiff left right deletion" style="background-color: #fac5cd;">0</span></span></span>

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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

7

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">.. versionchanged:: 5.4.<span class="idiff left right addition" style="background-color: #c7f0d2;">7</span></span></span>

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8

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

8

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

9

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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right deletion" style="background-color: #fac5cd;">2</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

9

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right addition" style="background-color: #c7f0d2;">3</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10" class="line" lang="python"><span class="s" style="color: #d14;">Licensed under the MIT license. See LICENSE.md file.</span></span>

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC11" class="line" lang="python"></span>

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="372" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="372" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -372,6 +372,7 @@ class GenomeAnalysisEukaryotesMetaeuk(GenomeAnalysisEukaryotes):</td>

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<td class="new_line diff-line-num" data-linenumber="372" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC372" class="line" lang="python">        <span class="nf" style="color: #900; font-weight: 600;">super</span><span class="p">().</span><span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">()</span></span>

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<td class="old_line diff-line-num" data-linenumber="373" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="373" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC373" class="line" lang="python">        <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">metaeuk_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

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<td class="old_line diff-line-num" data-linenumber="374" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="374" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC374" class="line" lang="python">        <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_details</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

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<td class="old_line diff-line-num new" data-linenumber="375" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="375" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC375" class="line" lang="python">        <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_update_mapping</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="376" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC376" class="line" lang="python"></span>

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<td class="new_line diff-line-num" data-linenumber="377" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC377" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">init_tools</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC378" class="line" lang="python">        <span class="nf" style="color: #900; font-weight: 600;">super</span><span class="p">().</span><span class="nf" style="color: #900; font-weight: 600;">init_tools</span><span class="p">()</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="498" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -498,8 +499,13 @@ class GenomeAnalysisEukaryotesMetaeuk(GenomeAnalysisEukaryotes):</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC499" class="line" lang="python">        <span class="n" style="color: #333;">exon_records</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<td class="new_line diff-line-num" data-linenumber="500" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC500" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">busco_id</span><span class="p">,</span> <span class="n" style="color: #333;">gene_match</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">busco_dict</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">items</span><span class="p">():</span></span>

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<td class="new_line diff-line-num" data-linenumber="501" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC501" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">gene_id</span><span class="p">,</span> <span class="n" style="color: #333;">details</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gene_match</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">items</span><span class="p">():</span></span>

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<td class="new_line diff-line-num old" data-linenumber="502" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC501" class="line" lang="python">                <span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">details</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="s" style="color: #d14;">"orig gene ID"</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">rsplit</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

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<td class="new_line diff-line-num old" data-linenumber="502" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC502" class="line" lang="python">                <span class="n" style="color: #333;">gene_start</span><span class="p">,</span> <span class="n" style="color: #333;">gene_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">coords</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="502" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC502" class="line" lang="python">                <span class="n" style="color: #333;">gene_start</span><span class="p">,</span> <span class="n" style="color: #333;">gene_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_id</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="503" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC503" class="line" lang="python">                <span class="n" style="color: #333;">low_coord</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">min</span><span class="p">([</span><span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">gene_start</span><span class="p">),</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">gene_end</span><span class="p">)])</span></span>

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<td class="new_line diff-line-num new" data-linenumber="504" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC504" class="line" lang="python">                <span class="n" style="color: #333;">high_coord</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">max</span><span class="p">([</span><span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">gene_start</span><span class="p">),</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">gene_end</span><span class="p">)])</span></span>

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<td class="new_line diff-line-num new" data-linenumber="505" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC505" class="line" lang="python">                <span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">orig_gene_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">details</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="s" style="color: #d14;">"orig gene ID"</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">rsplit</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="506" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC506" class="line" lang="python">                <span class="n" style="color: #333;">orig_gene_start</span><span class="p">,</span> <span class="n" style="color: #333;">orig_gene_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">orig_gene_coords</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC507" class="line" lang="python">                <span class="n" style="color: #333;">low_coord_orig</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">min</span><span class="p">([</span><span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">orig_gene_start</span><span class="p">),</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">orig_gene_end</span><span class="p">)])</span></span>

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<td class="old_line diff-line-num new" data-linenumber="503" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="508" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

508

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC508" class="line" lang="python">                <span class="n" style="color: #333;">high_coord_orig</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">max</span><span class="p">([</span><span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">orig_gene_start</span><span class="p">),</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">orig_gene_end</span><span class="p">)])</span></span>

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503

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<td class="new_line diff-line-num" data-linenumber="509" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

509

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC509" class="line" lang="python">                <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_details</span><span class="p">[</span><span class="n" style="color: #333;">gene_id</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="s" style="color: #d14;">"strand"</span><span class="p">]</span></span>

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<td class="old_line diff-line-num" data-linenumber="504" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

504

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<td class="new_line diff-line-num" data-linenumber="510" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC510" class="line" lang="python">                <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">details</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="s" style="color: #d14;">"bitscore"</span><span class="p">]</span></span>

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<td class="old_line diff-line-num" data-linenumber="505" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

505

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC511" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="524" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="530" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -524,7 +530,7 @@ class GenomeAnalysisEukaryotesMetaeuk(GenomeAnalysisEukaryotes):</td>

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524

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<td class="new_line diff-line-num" data-linenumber="530" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

530

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC530" class="line" lang="python">                            <span class="p">[</span></span>

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<td class="old_line diff-line-num" data-linenumber="525" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

525

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<td class="new_line diff-line-num" data-linenumber="531" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC531" class="line" lang="python">                                <span class="s" style="color: #d14;">"grep"</span><span class="p">,</span></span>

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526

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<td class="new_line diff-line-num" data-linenumber="532" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

532

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC532" class="line" lang="python">                                <span class="s" style="color: #d14;">"{}|{}|.*|{}|{}|"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>

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<td class="old_line diff-line-num old" data-linenumber="527" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

527

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<td class="new_line diff-line-num old" data-linenumber="533" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC527" class="line" lang="python">                                    <span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">gene_start</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff right deletion" style="background-color: #fac5cd;">gene_end</span></span></span>

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<td class="new_line diff-line-num new" data-linenumber="533" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

533

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC533" class="line" lang="python">                                    <span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left addition" style="background-color: #c7f0d2;">low_coord_orig</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff right addition" style="background-color: #c7f0d2;">high_coord_orig</span></span></span>

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528

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<td class="new_line diff-line-num" data-linenumber="534" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

534

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC534" class="line" lang="python">                                <span class="p">),</span></span>

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529

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<td class="new_line diff-line-num" data-linenumber="535" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC535" class="line" lang="python">                                <span class="n" style="color: #333;">rerun_results</span><span class="p">,</span></span>

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530

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC536" class="line" lang="python">                            <span class="p">]</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="534" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="540" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -534,7 +540,7 @@ class GenomeAnalysisEukaryotesMetaeuk(GenomeAnalysisEukaryotes):</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC540" class="line" lang="python">                            <span class="p">[</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC541" class="line" lang="python">                                <span class="s" style="color: #d14;">"grep"</span><span class="p">,</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC542" class="line" lang="python">                                <span class="s" style="color: #d14;">"{}|{}|.*|{}|{}|"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>

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<td class="new_line diff-line-num old" data-linenumber="543" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC537" class="line" lang="python">                                    <span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">gene_start</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">,</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff right deletion" style="background-color: #fac5cd;">gene_end</span></span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC543" class="line" lang="python">                                    <span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left addition" style="background-color: #c7f0d2;">low_coord_orig</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff right addition" style="background-color: #c7f0d2;">high_coord_orig</span></span></span>

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538

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC544" class="line" lang="python">                                <span class="p">),</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC545" class="line" lang="python">                                <span class="n" style="color: #333;">initial_run_results</span><span class="p">,</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC546" class="line" lang="python">                            <span class="p">]</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="552" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -552,19 +558,22 @@ class GenomeAnalysisEukaryotesMetaeuk(GenomeAnalysisEukaryotes):</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC558" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># redundantly matches the gene coordinates again.</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC559" class="line" lang="python">                <span class="n" style="color: #333;">good_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">metaeuk_runner</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find_match</span><span class="p">(</span></span>

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554

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC560" class="line" lang="python">                    <span class="n" style="color: #333;">matches</span><span class="p">,</span></span>

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555

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC555" class="line" lang="python">                    <span class="p">[</span><span class="s" style="color: #d14;">"|{}|"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">gene_start</span><span class="p">),</span> <span class="s" style="color: #d14;">"|{}|"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">gene_end</span><span class="p">),</span> <span class="n" style="color: #333;">sequence</span><span class="p">],</span></span>

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561

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC561" class="line" lang="python">                    <span class="p">[</span><span class="s" style="color: #d14;">"|{}|"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left addition" style="background-color: #c7f0d2;">orig_</span>gene_start</span><span class="p">),</span> <span class="s" style="color: #d14;">"|{}|"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff right addition" style="background-color: #c7f0d2;">orig_</span>gene_end</span><span class="p">),</span> <span class="n" style="color: #333;">sequence</span><span class="p">],</span></span>

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556

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC562" class="line" lang="python">                <span class="p">)</span></span>

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557

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563

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC563" class="line" lang="python"></span>

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558

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<td class="new_line diff-line-num" data-linenumber="564" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC564" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">good_match</span><span class="p">:</span></span>

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559

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<td class="new_line diff-line-num" data-linenumber="565" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

565

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC565" class="line" lang="python">                    <span class="n" style="color: #333;">low_coords</span><span class="p">,</span> <span class="n" style="color: #333;">high_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">metaeuk_runner</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">extract_exon_coords</span><span class="p">(</span></span>

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560

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566

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC566" class="line" lang="python">                        <span class="n" style="color: #333;">good_match</span></span>

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561

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567

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC567" class="line" lang="python">                    <span class="p">)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="562" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

562

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<td class="new_line diff-line-num old" data-linenumber="568" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC562" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">low_coords</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">high_coords</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span>  <span class="c1" style="color: #998; font-style: italic;"># for negative strand exons the order is reversed</span></span>

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568

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC568" class="line" lang="python">                    <span class="nf" style="color: #900; font-weight: 600;">if </span><span class="p">(</span></span>

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<td class="new_line diff-line-num new" data-linenumber="569" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

569

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC569" class="line" lang="python">                        <span class="n" style="color: #333;">low_coords</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">high_coords</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

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<td class="new_line diff-line-num new" data-linenumber="570" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

570

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC570" class="line" lang="python">                    <span class="p">):</span>  <span class="c1" style="color: #998; font-style: italic;"># for negative strand exons the order is reversed</span></span>

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563

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC571" class="line" lang="python">                        <span class="n" style="color: #333;">low_coords</span><span class="p">,</span> <span class="n" style="color: #333;">high_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">high_coords</span><span class="p">,</span> <span class="n" style="color: #333;">low_coords</span></span>

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<td class="old_line diff-line-num old" data-linenumber="564" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

564

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<td class="new_line diff-line-num old" data-linenumber="572" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC564" class="line" lang="python">                    <span class="n" style="color: #333;">trimmed_low</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">gene_id</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>

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565

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<td class="new_line diff-line-num old" data-linenumber="572" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC565" class="line" lang="python">                    <span class="n" style="color: #333;">trimmed_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">gene_id</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>

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572

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC572" class="line" lang="python"></span>

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566

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC573" class="line" lang="python">                    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">entry</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nf" style="color: #900; font-weight: 600;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">low_coords</span><span class="p">):</span></span>

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567

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<td class="new_line diff-line-num old" data-linenumber="574" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC567" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">trimmed_low</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">trimmed_high</span><span class="p">:</span>  <span class="c1" style="color: #998; font-style: italic;"># don't include exons that were previously removed due to overlaps</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC574" class="line" lang="python">                        <span class="nf" style="color: #900; font-weight: 600;">if </span><span class="p">(</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC575" class="line" lang="python">                            <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">low_coord</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">high_coord</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC576" class="line" lang="python">                        <span class="p">):</span>  <span class="c1" style="color: #998; font-style: italic;"># don't include exons that were previously removed due to overlaps</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC577" class="line" lang="python">                            <span class="k" style="font-weight: 600;">continue</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC578" class="line" lang="python">                        <span class="n" style="color: #333;">record</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC579" class="line" lang="python">                            <span class="n" style="color: #333;">busco_id</span><span class="p">,</span></span>

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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -574,7 +583,7 @@ class GenomeAnalysisEukaryotesMetaeuk(GenomeAnalysisEukaryotes):</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC583" class="line" lang="python">                            <span class="n" style="color: #333;">strand</span><span class="p">,</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC584" class="line" lang="python">                            <span class="n" style="color: #333;">score</span><span class="p">,</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC585" class="line" lang="python">                            <span class="n" style="color: #333;">run_found</span><span class="p">,</span></span>

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577

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC577" class="line" lang="python">                            <span class="n" style="color: #333;"><span class="idiff left right deletion" style="background-color: #fac5cd;">gene_id</span></span><span class="p">,</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC586" class="line" lang="python">                            <span class="n" style="color: #333;"><span class="idiff left addition" style="background-color: #c7f0d2;">details</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition" style="background-color: #c7f0d2;">0</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">][</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"orig gene ID"</span></span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">]</span>,</span></span>

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587

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC587" class="line" lang="python">                        <span class="p">)</span></span>

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579

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<td class="new_line diff-line-num" data-linenumber="588" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

588

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC588" class="line" lang="python">                        <span class="n" style="color: #333;">exon_records</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="580" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

580

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<td class="new_line diff-line-num" data-linenumber="589" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

589

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC589" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">exon_records</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="592" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="601" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -592,36 +601,50 @@ class GenomeAnalysisEukaryotesMetaeuk(GenomeAnalysisEukaryotes):</td>

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<td class="old_line diff-line-num" data-linenumber="592" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

592

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<td class="new_line diff-line-num" data-linenumber="601" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC601" class="line" lang="python">            <span class="n" style="color: #333;">busco_gene_groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">busco_group</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">groupby</span><span class="p">(</span><span class="s" style="color: #d14;">"Orig gene ID"</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="593" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

593

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<td class="new_line diff-line-num" data-linenumber="602" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC602" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">gene_match</span><span class="p">,</span> <span class="n" style="color: #333;">busco_gene_group</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">busco_gene_groups</span><span class="p">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="594" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

594

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<td class="new_line diff-line-num" data-linenumber="603" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

603

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC603" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gene_match</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">matches</span><span class="p">:</span></span>

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<td class="old_line diff-line-num old" data-linenumber="595" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

595

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<td class="new_line diff-line-num old" data-linenumber="604" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC595" class="line" lang="python">                    <span class="k" style="font-weight: 600;">continue</span></span>

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<td class="old_line diff-line-num old" data-linenumber="596" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

596

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<td class="new_line diff-line-num old" data-linenumber="604" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC596" class="line" lang="python">                <span class="n" style="color: #333;">new_gene_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_match</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)[</span></span>

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<td class="old_line diff-line-num old" data-linenumber="597" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

597

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<td class="new_line diff-line-num old" data-linenumber="604" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC597" class="line" lang="python">                    <span class="mi" style="color: #099;">0</span></span>

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<td class="old_line diff-line-num old" data-linenumber="598" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

598

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<td class="new_line diff-line-num old" data-linenumber="604" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC598" class="line" lang="python">                <span class="p">]</span>  <span class="c1" style="color: #998; font-style: italic;"># these two lines are not really used - they just initialize values that will be changed</span></span>

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<td class="old_line diff-line-num old" data-linenumber="599" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

599

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<td class="new_line diff-line-num old" data-linenumber="604" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC599" class="line" lang="python">                <span class="n" style="color: #333;">new_gene_stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_match</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="600" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="604" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

604

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC604" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">busco_id</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_update_mapping</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="600" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="605" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

605

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC605" class="line" lang="python">                        <span class="k" style="font-weight: 600;">continue</span></span>

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<td class="old_line diff-line-num new" data-linenumber="600" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="606" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

606

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC606" class="line" lang="python">                    <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">gene_match</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_update_mapping</span><span class="p">[</span><span class="n" style="color: #333;">busco_id</span><span class="p">]:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="600" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="607" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

607

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC607" class="line" lang="python">                        <span class="k" style="font-weight: 600;">continue</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="600" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="608" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

608

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC608" class="line" lang="python">                    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="600" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="609" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

609

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC609" class="line" lang="python">                        <span class="n" style="color: #333;">gene_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_update_mapping</span><span class="p">[</span><span class="n" style="color: #333;">busco_id</span><span class="p">][</span><span class="n" style="color: #333;">gene_match</span><span class="p">][</span><span class="s" style="color: #d14;">"new_gene_coords"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="600" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="610" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

610

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC610" class="line" lang="python">                <span class="n" style="color: #333;">new_gene_start</span><span class="p">,</span> <span class="n" style="color: #333;">new_gene_stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_match</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># this line just initializes values that will be changed if an exon is removed</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="600" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

600

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<td class="new_line diff-line-num" data-linenumber="611" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

611

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC611" class="line" lang="python">                <span class="n" style="color: #333;">start_trim</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="601" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

601

</td>

<td class="new_line diff-line-num" data-linenumber="612" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

612

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC612" class="line" lang="python">                <span class="n" style="color: #333;">end_trim</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="602" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

602

</td>

<td class="new_line diff-line-num" data-linenumber="613" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

613

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC613" class="line" lang="python">                <span class="n" style="color: #333;">group_indices</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">set</span><span class="p">(</span><span class="n" style="color: #333;">busco_gene_group</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="603" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

603

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<td class="new_line diff-line-num" data-linenumber="614" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

614

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC614" class="line" lang="python">                <span class="n" style="color: #333;">intersection</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">group_indices</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">intersection</span><span class="p">(</span><span class="n" style="color: #333;">inds_to_remove</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="604" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

604

</td>

<td class="new_line diff-line-num" data-linenumber="615" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

615

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC615" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">intersection</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="605" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="616" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

616

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC616" class="line" lang="python">                    <span class="n" style="color: #333;">new_gene_low</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">min</span><span class="p">(</span><span class="n" style="color: #333;">new_gene_start</span><span class="p">,</span> <span class="n" style="color: #333;">new_gene_stop</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># initialize values</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="605" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="617" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

617

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC617" class="line" lang="python">                    <span class="n" style="color: #333;">new_gene_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">max</span><span class="p">(</span><span class="n" style="color: #333;">new_gene_start</span><span class="p">,</span> <span class="n" style="color: #333;">new_gene_stop</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="605" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

605

</td>

<td class="new_line diff-line-num" data-linenumber="618" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

618

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC618" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">intersection</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">group_indices</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="606" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

606

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<td class="new_line diff-line-num" data-linenumber="619" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

619

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC619" class="line" lang="python">                        <span class="k" style="font-weight: 600;">continue</span>  <span class="c1" style="color: #998; font-style: italic;"># remove entire gene - don't add to new dict</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="607" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

607

</td>

<td class="new_line diff-line-num old" data-linenumber="620" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC607" class="line" lang="python">                    <span class="n" style="color: #333;">ordered_exons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">busco_gene_group</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">sort_values</span><span class="p">(</span><span class="n" style="color: #333;">by</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Start"</span><span class="p">).</span><span class="nf" style="color: #900; font-weight: 600;">reset_index</span><span class="p">()</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="608" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="620" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

620

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC620" class="line" lang="python">                    <span class="n" style="color: #333;">ordered_exons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">busco_gene_group</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">sort_values</span><span class="p">(</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="608" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="621" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

621

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC621" class="line" lang="python">                        <span class="n" style="color: #333;">by</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Low coord"</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="608" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="622" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

622

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC622" class="line" lang="python">                    <span class="p">).</span><span class="nf" style="color: #900; font-weight: 600;">reset_index</span><span class="p">()</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="608" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

608

</td>

<td class="new_line diff-line-num" data-linenumber="623" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

623

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC623" class="line" lang="python">                    <span class="n" style="color: #333;">new_indices</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ordered_exons</span><span class="p">.</span><span class="n" style="color: #333;">index</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="609" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

609

</td>

<td class="new_line diff-line-num" data-linenumber="624" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

624

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC624" class="line" lang="python">                    <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ordered_exons</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="s" style="color: #d14;">"Sequence"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="610" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="625" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

625

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC625" class="line" lang="python">                    <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ordered_exons</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="s" style="color: #d14;">"Strand"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="610" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

610

</td>

<td class="new_line diff-line-num" data-linenumber="626" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

626

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC626" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="611" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

611

</td>

<td class="new_line diff-line-num" data-linenumber="627" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

627

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC627" class="line" lang="python">                    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new_indices</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="612" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

612

</td>

<td class="new_line diff-line-num" data-linenumber="628" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

628

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC628" class="line" lang="python">                        <span class="n" style="color: #333;">old_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ordered_exons</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">][</span><span class="s" style="color: #d14;">"index"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="613" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

613

</td>

<td class="new_line diff-line-num" data-linenumber="629" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

629

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC629" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">old_index</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">intersection</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="614" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

614

</td>

<td class="new_line diff-line-num old" data-linenumber="630" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC614" class="line" lang="python">                            <span class="n" style="color: #333;">start_trim</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">discarded_exon_lengths</span><span class="p">[</span><span class="n" style="color: #333;">old_index</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="615" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="630" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

630

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC630" class="line" lang="python">                            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"+"</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="615" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="631" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

631

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC631" class="line" lang="python">                                <span class="n" style="color: #333;">start_trim</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">discarded_exon_lengths</span><span class="p">[</span><span class="n" style="color: #333;">old_index</span><span class="p">]</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="615" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="632" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

632

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC632" class="line" lang="python">                            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="615" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="633" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

633

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC633" class="line" lang="python">                                <span class="n" style="color: #333;">end_trim</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">discarded_exon_lengths</span><span class="p">[</span><span class="n" style="color: #333;">old_index</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="615" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

615

</td>

<td class="new_line diff-line-num" data-linenumber="634" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

634

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC634" class="line" lang="python">                        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="616" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

616

</td>

<td class="new_line diff-line-num old" data-linenumber="635" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC616" class="line" lang="python">                            <span class="n" style="color: #333;">new_gene_<span class="idiff left deletion" style="background-color: #fac5cd;">start</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">old_index</span><span class="p">][</span><span class="s" style="color: #d14;">"<span class="idiff right deletion" style="background-color: #fac5cd;">Start</span>"</span><span class="p">]</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="617" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="635" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

635

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC635" class="line" lang="python">                            <span class="n" style="color: #333;">new_gene_<span class="idiff left addition" style="background-color: #c7f0d2;">low</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">old_index</span><span class="p">][</span><span class="s" style="color: #d14;">"<span class="idiff right addition" style="background-color: #c7f0d2;">Low coord</span>"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="617" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

617

</td>

<td class="new_line diff-line-num" data-linenumber="636" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

636

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC636" class="line" lang="python">                            <span class="k" style="font-weight: 600;">break</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="618" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

618

</td>

<td class="new_line diff-line-num" data-linenumber="637" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

637

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC637" class="line" lang="python">                    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new_indices</span><span class="p">[::</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]:</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="619" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

619

</td>

<td class="new_line diff-line-num" data-linenumber="638" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

638

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC638" class="line" lang="python">                        <span class="n" style="color: #333;">old_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ordered_exons</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">][</span><span class="s" style="color: #d14;">"index"</span><span class="p">]</span></span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="620" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

620

</td>

<td class="new_line diff-line-num" data-linenumber="639" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

639

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC639" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">old_index</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">intersection</span><span class="p">:</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="621" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

621

</td>

<td class="new_line diff-line-num old" data-linenumber="640" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC621" class="line" lang="python">                            <span class="n" style="color: #333;">end_trim</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">discarded_exon_lengths</span><span class="p">[</span><span class="n" style="color: #333;">old_index</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="622" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="640" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

640

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC640" class="line" lang="python">                            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"+"</span><span class="p">:</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="622" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="641" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

641

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC641" class="line" lang="python">                                <span class="n" style="color: #333;">end_trim</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">discarded_exon_lengths</span><span class="p">[</span><span class="n" style="color: #333;">old_index</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="622" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="642" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

642

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC642" class="line" lang="python">                            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="622" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="643" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

643

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC643" class="line" lang="python">                                <span class="n" style="color: #333;">start_trim</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">discarded_exon_lengths</span><span class="p">[</span><span class="n" style="color: #333;">old_index</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="622" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

622

</td>

<td class="new_line diff-line-num" data-linenumber="644" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

644

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC644" class="line" lang="python">                        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="623" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

623

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<td class="new_line diff-line-num old" data-linenumber="645" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC623" class="line" lang="python">                            <span class="n" style="color: #333;">new_gene_<span class="idiff left deletion" style="background-color: #fac5cd;">stop</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">old_index</span><span class="p">][</span><span class="s" style="color: #d14;">"<span class="idiff right deletion" style="background-color: #fac5cd;">Stop</span>"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="624" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="645" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

645

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC645" class="line" lang="python">                            <span class="n" style="color: #333;">new_gene_<span class="idiff left addition" style="background-color: #c7f0d2;">high</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">old_index</span><span class="p">][</span><span class="s" style="color: #d14;">"<span class="idiff right addition" style="background-color: #c7f0d2;">High coord</span>"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="624" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

624

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<td class="new_line diff-line-num" data-linenumber="646" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

646

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC646" class="line" lang="python">                            <span class="k" style="font-weight: 600;">break</span></span>

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<td class="old_line diff-line-num new" data-linenumber="625" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="647" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

647

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC647" class="line" lang="python">                    <span class="n" style="color: #333;">new_gene_start</span><span class="p">,</span> <span class="n" style="color: #333;">new_gene_stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">new_gene_low</span><span class="p">,</span> <span class="n" style="color: #333;">new_gene_high</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"+"</span> <span class="nf" style="color: #900; font-weight: 600;">else </span><span class="p">(</span><span class="n" style="color: #333;">new_gene_high</span><span class="p">,</span> <span class="n" style="color: #333;">new_gene_low</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="625" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

625

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<td class="new_line diff-line-num" data-linenumber="648" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

648

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC648" class="line" lang="python">                    <span class="n" style="color: #333;">new_gene_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{}:{}-{}"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="626" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

626

</td>

<td class="new_line diff-line-num" data-linenumber="649" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

649

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC649" class="line" lang="python">                        <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">new_gene_start</span><span class="p">,</span> <span class="n" style="color: #333;">new_gene_stop</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="627" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

627

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<td class="new_line diff-line-num" data-linenumber="650" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

650

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC650" class="line" lang="python">                    <span class="p">)</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="634" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="657" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -634,19 +657,24 @@ class GenomeAnalysisEukaryotesMetaeuk(GenomeAnalysisEukaryotes):</td>

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<td class="old_line diff-line-num" data-linenumber="634" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

634

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<td class="new_line diff-line-num" data-linenumber="657" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

657

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC657" class="line" lang="python">                <span class="n" style="color: #333;">matched_genes_new</span><span class="p">[</span><span class="n" style="color: #333;">new_gene_match</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">busco_id</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="635" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

635

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<td class="new_line diff-line-num" data-linenumber="658" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

658

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC658" class="line" lang="python">                <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_details</span><span class="p">[</span><span class="n" style="color: #333;">new_gene_match</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="636" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

636

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<td class="new_line diff-line-num" data-linenumber="659" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

659

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC659" class="line" lang="python">                    <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="637" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

637

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<td class="new_line diff-line-num old" data-linenumber="660" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC637" class="line" lang="python">                        <span class="s" style="color: #d14;">"gene_start"</span><span class="p">:</span> <span class="n" style="color: #333;">new_gene_start</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="638" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="660" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

660

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC660" class="line" lang="python">                        <span class="s" style="color: #d14;">"gene_start"</span><span class="p">:</span> <span class="n" style="color: #333;">new_gene_start</span><span class="p">,</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition" style="background-color: #c7f0d2;"># these are the same as the old gene coordinates if no exons were removed</span></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="638" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

638

</td>

<td class="new_line diff-line-num" data-linenumber="661" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

661

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC661" class="line" lang="python">                        <span class="s" style="color: #d14;">"gene_end"</span><span class="p">:</span> <span class="n" style="color: #333;">new_gene_stop</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="639" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

639

</td>

<td class="new_line diff-line-num" data-linenumber="662" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

662

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC662" class="line" lang="python">                        <span class="s" style="color: #d14;">"strand"</span><span class="p">:</span> <span class="n" style="color: #333;">df_strand</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="640" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

640

</td>

<td class="new_line diff-line-num" data-linenumber="663" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

663

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC663" class="line" lang="python">                    <span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="641" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

641

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<td class="new_line diff-line-num" data-linenumber="664" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

664

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC664" class="line" lang="python">                <span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="642" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

642

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<td class="new_line diff-line-num" data-linenumber="665" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

665

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC665" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">new_gene_match</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">gene_match</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="643" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

643

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<td class="new_line diff-line-num" data-linenumber="666" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

666

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC666" class="line" lang="python">                    <span class="n" style="color: #333;">trimmed_sequence_aa</span><span class="p">,</span> <span class="n" style="color: #333;">trimmed_sequence_nt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">trim_sequence</span><span class="p">(</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="644" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

644

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<td class="new_line diff-line-num old" data-linenumber="667" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC644" class="line" lang="python">                        <span class="n" style="color: #333;">gene_match</span><span class="p">,</span> <span class="n" style="color: #333;">start_trim</span><span class="p">,</span> <span class="n" style="color: #333;">end_trim</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="645" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="667" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

667

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC667" class="line" lang="python">                        <span class="n" style="color: #333;">gene_match</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left addition" style="background-color: #c7f0d2;">new_gene_match</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">start_trim</span><span class="p">,</span> <span class="n" style="color: #333;">end_trim</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="645" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

645

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<td class="new_line diff-line-num" data-linenumber="668" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

668

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC668" class="line" lang="python">                    <span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="646" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="669" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

669

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC669" class="line" lang="python">                    <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_update_mapping</span><span class="p">[</span><span class="n" style="color: #333;">busco_id</span><span class="p">][</span><span class="n" style="color: #333;">gene_match</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"new_gene_coords"</span><span class="p">:</span> <span class="n" style="color: #333;">new_gene_match</span><span class="p">,</span> <span class="s" style="color: #d14;">"start_trim"</span><span class="p">:</span> <span class="n" style="color: #333;">start_trim</span><span class="p">,</span> <span class="s" style="color: #d14;">"end_trim"</span><span class="p">:</span> <span class="n" style="color: #333;">end_trim</span><span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="646" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

646

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<td class="new_line diff-line-num" data-linenumber="670" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

670

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC670" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="647" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

647

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<td class="new_line diff-line-num" data-linenumber="671" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

671

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC671" class="line" lang="python">                    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="648" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

648

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</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC648" class="line" lang="python">                        <span class="n" style="color: #333;">trimmed_sequence_aa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">metaeuk_runner</span><span class="p">.</span><span class="n" style="color: #333;">sequences_aa</span><span class="p">[</span><span class="n" style="color: #333;">gene_match</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="649" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

649

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<td class="new_line diff-line-num old" data-linenumber="672" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC649" class="line" lang="python">                        <span class="n" style="color: #333;">trimmed_sequence_nt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">metaeuk_runner</span><span class="p">.</span><span class="n" style="color: #333;">sequences_nt</span><span class="p">[</span><span class="n" style="color: #333;">gene_match</span><span class="p">]</span></span>

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<td class="new_line diff-line-num new" data-linenumber="672" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

672

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC672" class="line" lang="python">                        <span class="n" style="color: #333;">trimmed_sequence_aa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">metaeuk_runner</span><span class="p">.</span><span class="n" style="color: #333;">sequences_aa</span><span class="p">[</span></span>

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<td class="old_line diff-line-num new" data-linenumber="650" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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673

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC673" class="line" lang="python">                            <span class="n" style="color: #333;">gene_match</span></span>

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<td class="new_line diff-line-num new" data-linenumber="674" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

674

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC674" class="line" lang="python">                        <span class="p">]</span></span>

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<td class="new_line diff-line-num new" data-linenumber="675" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

675

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC675" class="line" lang="python">                        <span class="n" style="color: #333;">trimmed_sequence_nt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">metaeuk_runner</span><span class="p">.</span><span class="n" style="color: #333;">sequences_nt</span><span class="p">[</span></span>

</pre></td>

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676

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC676" class="line" lang="python">                            <span class="n" style="color: #333;">gene_match</span></span>

</pre></td>

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677

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC677" class="line" lang="python">                        <span class="p">]</span></span>

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650

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<td class="new_line diff-line-num" data-linenumber="678" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

678

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC678" class="line" lang="python">                    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span>  <span class="c1" style="color: #998; font-style: italic;"># happens on the second run if the first run trimmed the sequence already</span></span>

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<td class="old_line diff-line-num" data-linenumber="651" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

651

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<td class="new_line diff-line-num" data-linenumber="679" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

679

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC679" class="line" lang="python">                        <span class="n" style="color: #333;">trimmed_sequence_aa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_aa</span><span class="p">[</span><span class="n" style="color: #333;">gene_match</span><span class="p">]</span></span>

</pre></td>

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652

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<td class="new_line diff-line-num" data-linenumber="680" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC680" class="line" lang="python">                        <span class="n" style="color: #333;">trimmed_sequence_nt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_nt</span><span class="p">[</span><span class="n" style="color: #333;">gene_match</span><span class="p">]</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="654" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="682" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -654,9 +682,9 @@ class GenomeAnalysisEukaryotesMetaeuk(GenomeAnalysisEukaryotes):</td>

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654

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC682" class="line" lang="python">                <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_nt</span><span class="p">[</span><span class="n" style="color: #333;">new_gene_match</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trimmed_sequence_nt</span></span>

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655

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<td class="new_line diff-line-num" data-linenumber="683" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC683" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">hmmer_result_dict_new</span><span class="p">,</span> <span class="n" style="color: #333;">matched_genes_new</span></span>

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656

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC684" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="657" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

657

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<td class="new_line diff-line-num old" data-linenumber="685" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC657" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">trim_sequence</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">old_gene_match</span><span class="p">,</span> <span class="n" style="color: #333;">start_trim</span><span class="p">,</span> <span class="n" style="color: #333;">end_trim</span><span class="p">):</span></span>

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<td class="old_line diff-line-num old" data-linenumber="658" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

658

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<td class="new_line diff-line-num old" data-linenumber="685" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC658" class="line" lang="python">        <span class="n" style="color: #333;">old_sequence_aa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">metaeuk_runner</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">.</span></span><span class="n" style="color: #333;">sequences_aa</span><span class="p">[</span><span class="n" style="color: #333;">old_gene_match</span><span class="p">]</span></span>

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<td class="old_line diff-line-num old" data-linenumber="659" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

659

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<td class="new_line diff-line-num old" data-linenumber="685" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC659" class="line" lang="python">        <span class="n" style="color: #333;">old_sequence_nt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">metaeuk_runner</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">.</span></span><span class="n" style="color: #333;">sequences_nt</span><span class="p">[</span><span class="n" style="color: #333;">old_gene_match</span><span class="p">]</span></span>

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<td class="old_line diff-line-num new" data-linenumber="660" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="685" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

685

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC685" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">trim_sequence</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">old_gene_match</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left addition" style="background-color: #c7f0d2;">new_gene_match</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">start_trim</span><span class="p">,</span> <span class="n" style="color: #333;">end_trim</span><span class="p">):</span></span>

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<td class="old_line diff-line-num new" data-linenumber="660" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="686" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

686

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC686" class="line" lang="python">        <span class="n" style="color: #333;">old_sequence_aa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_aa</span><span class="p">[</span><span class="n" style="color: #333;">old_gene_match</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="660" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="687" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

687

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC687" class="line" lang="python">        <span class="n" style="color: #333;">old_sequence_nt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_nt</span><span class="p">[</span><span class="n" style="color: #333;">old_gene_match</span><span class="p">]</span></span>

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660

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<td class="new_line diff-line-num" data-linenumber="688" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC688" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="661" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

661

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<td class="new_line diff-line-num" data-linenumber="689" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC689" class="line" lang="python">        <span class="n" style="color: #333;">new_sequence_nt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">old_sequence_nt</span><span class="p">[</span><span class="n" style="color: #333;">start_trim</span> <span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">old_sequence_nt</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">end_trim</span><span class="p">]</span></span>

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662

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<td class="new_line diff-line-num" data-linenumber="690" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC690" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start_trim</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">end_trim</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="666" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="694" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -666,6 +694,8 @@ class GenomeAnalysisEukaryotesMetaeuk(GenomeAnalysisEukaryotes):</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC694" class="line" lang="python">        <span class="n" style="color: #333;">new_sequence_aa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">old_sequence_aa</span><span class="p">[</span></span>

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<td class="new_line diff-line-num" data-linenumber="695" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC695" class="line" lang="python">            <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">start_trim</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">old_sequence_aa</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">end_trim</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="696" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

696

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC696" class="line" lang="python">        <span class="p">]</span></span>

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<td class="old_line diff-line-num new" data-linenumber="669" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="697" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

697

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC697" class="line" lang="python">        <span class="n" style="color: #333;">new_sequence_nt</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_sequence_nt</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_sequence_nt</span><span class="p">.</span><span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_gene_match</span></span>

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<td class="new_line diff-line-num new" data-linenumber="698" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

698

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC698" class="line" lang="python">        <span class="n" style="color: #333;">new_sequence_aa</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_sequence_aa</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_sequence_aa</span><span class="p">.</span><span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_gene_match</span></span>

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669

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<td class="new_line diff-line-num" data-linenumber="699" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

699

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC699" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">new_sequence_aa</span><span class="p">,</span> <span class="n" style="color: #333;">new_sequence_nt</span></span>

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670

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<td class="new_line diff-line-num" data-linenumber="700" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC700" class="line" lang="python"></span>

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671

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<td class="new_line diff-line-num" data-linenumber="701" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC701" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">exons_to_df</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">records</span><span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="673" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="703" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -673,10 +703,11 @@ class GenomeAnalysisEukaryotesMetaeuk(GenomeAnalysisEukaryotes):</td>

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673

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC703" class="line" lang="python">            <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Validating exons and removing overlapping matches"</span><span class="p">)</span></span>

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674

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC704" class="line" lang="python"></span>

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<td class="new_line diff-line-num" data-linenumber="705" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC705" class="line" lang="python">        <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">metaeuk_runner</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">records_to_df</span><span class="p">(</span><span class="n" style="color: #333;">records</span><span class="p">)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="676" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

676

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<td class="new_line diff-line-num old" data-linenumber="706" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC676" class="line" lang="python">        <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left deletion" style="background-color: #fac5cd;">Start"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">]</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">=</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">df</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">[</span></span><span class="s" style="color: #d14;"><span class="idiff right deletion" style="background-color: #fac5cd;">"Start</span>"</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">astype</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>

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677

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<td class="new_line diff-line-num old" data-linenumber="706" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC677" class="line" lang="python">        <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left deletion" style="background-color: #fac5cd;">Stop"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">]</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">=</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">df</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">[</span></span><span class="s" style="color: #d14;"><span class="idiff right deletion" style="background-color: #fac5cd;">"Stop</span>"</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">astype</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>

</pre></td>

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706

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC706" class="line" lang="python">        <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left addition" style="background-color: #c7f0d2;">Low coord"</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">]</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">df</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">[</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"Low coord</span>"</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">astype</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="678" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="707" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

707

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC707" class="line" lang="python">        <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left addition" style="background-color: #c7f0d2;">High coord"</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">]</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">df</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">[</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"High coord</span>"</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">astype</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>

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678

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<td class="new_line diff-line-num" data-linenumber="708" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

708

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC708" class="line" lang="python">        <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"Score"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"Score"</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">astype</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="679" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

679

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<td class="new_line diff-line-num" data-linenumber="709" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

709

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC709" class="line" lang="python">        <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"Run found"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"Run found"</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">astype</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="710" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

710

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC710" class="line" lang="python">        <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">sort_values</span><span class="p">(</span><span class="n" style="color: #333;">by</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"Busco id"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Sequence"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Low coord"</span><span class="p">],</span> <span class="n" style="color: #333;">inplace</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

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680

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<td class="new_line diff-line-num" data-linenumber="711" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

711

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC711" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">df</span></span>

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681

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<td class="new_line diff-line-num" data-linenumber="712" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

712

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC712" class="line" lang="python"></span>

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682

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<td class="new_line diff-line-num" data-linenumber="713" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

713

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC713" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">find_overlaps</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">df</span><span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="700" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="731" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -700,7 +731,7 @@ class GenomeAnalysisEukaryotesMetaeuk(GenomeAnalysisEukaryotes):</td>

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700

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<td class="new_line diff-line-num" data-linenumber="731" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

731

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC731" class="line" lang="python">                <span class="n" style="color: #333;">bad_inds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">handle_diff_busco_overlap</span><span class="p">(</span><span class="n" style="color: #333;">overlap_inds</span><span class="p">,</span> <span class="n" style="color: #333;">df</span><span class="p">)</span></span>

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701

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<td class="new_line diff-line-num" data-linenumber="732" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

732

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC732" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">bad_inds</span><span class="p">:</span></span>

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702

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<td class="new_line diff-line-num" data-linenumber="733" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

733

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC733" class="line" lang="python">                    <span class="n" style="color: #333;">discarded_exon_lengths</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>

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703

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<td class="new_line diff-line-num old" data-linenumber="734" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC703" class="line" lang="python">                        <span class="nf" style="color: #900; font-weight: 600;">abs</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">i</span>loc</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">][</span><span class="s" style="color: #d14;">"<span class="idiff deletion" style="background-color: #fac5cd;">Stop</span>"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff deletion" style="background-color: #fac5cd;">i</span>loc</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">][</span><span class="s" style="color: #d14;">"<span class="idiff right deletion" style="background-color: #fac5cd;">Start</span>"</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="704" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="734" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

734

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC734" class="line" lang="python">                        <span class="nf" style="color: #900; font-weight: 600;">abs</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">][</span><span class="s" style="color: #d14;">"<span class="idiff left addition" style="background-color: #c7f0d2;">High coord</span>"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">][</span><span class="s" style="color: #d14;">"<span class="idiff right addition" style="background-color: #c7f0d2;">Low coord</span>"</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="704" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

704

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<td class="new_line diff-line-num" data-linenumber="735" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

735

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC735" class="line" lang="python">                    <span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="705" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

705

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<td class="new_line diff-line-num" data-linenumber="736" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

736

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC736" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">discarded_exon_lengths</span></span>

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<td class="old_line diff-line-num" data-linenumber="706" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

706

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<td class="new_line diff-line-num" data-linenumber="737" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

737

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC737" class="line" lang="python"></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="714" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="745" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -714,6 +745,8 @@ class GenomeAnalysisEukaryotesMetaeuk(GenomeAnalysisEukaryotes):</td>

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<td class="old_line diff-line-num" data-linenumber="714" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

714

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<td class="new_line diff-line-num" data-linenumber="745" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

745

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC745" class="line" lang="python">        <span class="n" style="color: #333;">busco_match2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match2</span><span class="p">[</span><span class="s" style="color: #d14;">"Busco id"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="715" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

715

</td>

<td class="new_line diff-line-num" data-linenumber="746" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

746

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC746" class="line" lang="python">        <span class="n" style="color: #333;">gene_match2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match2</span><span class="p">[</span><span class="s" style="color: #d14;">"Orig gene ID"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="716" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

716

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<td class="new_line diff-line-num" data-linenumber="747" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

747

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC747" class="line" lang="python">        <span class="n" style="color: #333;">run_match2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match2</span><span class="p">[</span><span class="s" style="color: #d14;">"Run found"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="717" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="748" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

748

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC748" class="line" lang="python">        <span class="n" style="color: #333;">strand1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match1</span><span class="p">[</span><span class="s" style="color: #d14;">"Strand"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="717" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="749" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

749

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC749" class="line" lang="python">        <span class="n" style="color: #333;">strand2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match2</span><span class="p">[</span><span class="s" style="color: #d14;">"Strand"</span><span class="p">]</span></span>

</pre></td>

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717

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<td class="new_line diff-line-num" data-linenumber="750" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC750" class="line" lang="python">        <span class="n" style="color: #333;">exons1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span></span>

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<td class="old_line diff-line-num" data-linenumber="718" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="751" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC751" class="line" lang="python">            <span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"Busco id"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">busco_match1</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="719" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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752

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC752" class="line" lang="python">            <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"Sequence"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">seq</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="744" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="777" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -744,30 +777,50 @@ class GenomeAnalysisEukaryotesMetaeuk(GenomeAnalysisEukaryotes):</td>

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744

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<td class="new_line diff-line-num" data-linenumber="777" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

777

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC777" class="line" lang="python">        <span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="745" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

745

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<td class="new_line diff-line-num" data-linenumber="778" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

778

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC778" class="line" lang="python">        <span class="n" style="color: #333;">gene_id1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match1</span><span class="p">[</span><span class="s" style="color: #d14;">"Orig gene ID"</span><span class="p">]</span></span>

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746

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<td class="new_line diff-line-num" data-linenumber="779" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

779

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC779" class="line" lang="python">        <span class="n" style="color: #333;">gene_id2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match2</span><span class="p">[</span><span class="s" style="color: #d14;">"Orig gene ID"</span><span class="p">]</span></span>

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<td class="new_line diff-line-num new" data-linenumber="780" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

780

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC780" class="line" lang="python"></span>

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<td class="old_line diff-line-num new" data-linenumber="747" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="781" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

781

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC781" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">busco_match1</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_update_mapping</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">gene_id1</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_update_mapping</span><span class="p">[</span><span class="n" style="color: #333;">busco_match1</span><span class="p">]:</span></span>

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<td class="new_line diff-line-num new" data-linenumber="782" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

782

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC782" class="line" lang="python">            <span class="n" style="color: #333;">start_trim1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_update_mapping</span><span class="p">[</span><span class="n" style="color: #333;">busco_match1</span><span class="p">][</span><span class="n" style="color: #333;">gene_id1</span><span class="p">][</span><span class="s" style="color: #d14;">"start_trim"</span><span class="p">]</span></span>

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<td class="new_line diff-line-num new" data-linenumber="783" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

783

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC783" class="line" lang="python">            <span class="n" style="color: #333;">end_trim1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_update_mapping</span><span class="p">[</span><span class="n" style="color: #333;">busco_match1</span><span class="p">][</span><span class="n" style="color: #333;">gene_id1</span><span class="p">][</span><span class="s" style="color: #d14;">"end_trim"</span><span class="p">]</span></span>

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<td class="new_line diff-line-num new" data-linenumber="784" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

784

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC784" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="old_line diff-line-num new" data-linenumber="747" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

785

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC785" class="line" lang="python">            <span class="n" style="color: #333;">start_trim1</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre></td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

786

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC786" class="line" lang="python">            <span class="n" style="color: #333;">end_trim1</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

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<td class="new_line diff-line-num new" data-linenumber="787" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

787

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC787" class="line" lang="python"></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="788" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

788

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC788" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">busco_match2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_update_mapping</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">gene_id2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_update_mapping</span><span class="p">[</span><span class="n" style="color: #333;">busco_match2</span><span class="p">]:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="747" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="789" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

789

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC789" class="line" lang="python">            <span class="n" style="color: #333;">start_trim2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_update_mapping</span><span class="p">[</span><span class="n" style="color: #333;">busco_match2</span><span class="p">][</span><span class="n" style="color: #333;">gene_id2</span><span class="p">][</span><span class="s" style="color: #d14;">"start_trim"</span><span class="p">]</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="747" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="790" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

790

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC790" class="line" lang="python">            <span class="n" style="color: #333;">end_trim2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_update_mapping</span><span class="p">[</span><span class="n" style="color: #333;">busco_match2</span><span class="p">][</span><span class="n" style="color: #333;">gene_id2</span><span class="p">][</span><span class="s" style="color: #d14;">"end_trim"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="747" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="791" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

791

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC791" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="747" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

792

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC792" class="line" lang="python">            <span class="n" style="color: #333;">start_trim2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="747" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="793" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

793

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC793" class="line" lang="python">            <span class="n" style="color: #333;">end_trim2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="747" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="794" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

794

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC794" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="747" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

747

</td>

<td class="new_line diff-line-num" data-linenumber="795" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

795

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC795" class="line" lang="python">        <span class="nf" style="color: #900; font-weight: 600;">if </span><span class="p">(</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="748" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

748

</td>

<td class="new_line diff-line-num" data-linenumber="796" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

796

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC796" class="line" lang="python">            <span class="n" style="color: #333;">hmmer_match_details1</span><span class="p">[</span><span class="n" style="color: #333;">gene_id1</span><span class="p">][</span><span class="s" style="color: #d14;">"score"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="749" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

749

</td>

<td class="new_line diff-line-num" data-linenumber="797" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

797

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC797" class="line" lang="python">            <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">hmmer_match_details2</span><span class="p">[</span><span class="n" style="color: #333;">gene_id2</span><span class="p">][</span><span class="s" style="color: #d14;">"score"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="750" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

750

</td>

<td class="new_line diff-line-num" data-linenumber="798" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

798

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC798" class="line" lang="python">        <span class="p">):</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="751" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

751

</td>

<td class="new_line diff-line-num" data-linenumber="799" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

799

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC799" class="line" lang="python">            <span class="n" style="color: #333;">priority_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hmmer_match_details1</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="752" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

752

</td>

<td class="new_line diff-line-num" data-linenumber="800" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

800

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC800" class="line" lang="python">            <span class="n" style="color: #333;">secondary_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hmmer_match_details2</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="753" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

753

</td>

<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC753" class="line" lang="python">            <span class="n" style="color: #333;">priority_exons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exons1</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="754" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

754

</td>

<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC754" class="line" lang="python">            <span class="n" style="color: #333;">secondary_exons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exons2</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="755" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="801" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

801

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC801" class="line" lang="python">            <span class="n" style="color: #333;">priority_exons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exons1</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">.</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">sort_values</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">by</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"Low coord"</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">ascending</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">strand1</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">==</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"+"</span></span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">)</span></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="755" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="802" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

802

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC802" class="line" lang="python">            <span class="n" style="color: #333;">secondary_exons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exons2</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">.</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">sort_values</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">by</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"Low coord"</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">ascending</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">strand2</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">==</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"+"</span></span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">)</span></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="755" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

755

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<td class="new_line diff-line-num" data-linenumber="803" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

803

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC803" class="line" lang="python">            <span class="n" style="color: #333;">priority_gene_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_id1</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="756" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

756

</td>

<td class="new_line diff-line-num" data-linenumber="804" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

804

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC804" class="line" lang="python">            <span class="n" style="color: #333;">secondary_gene_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_id2</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="757" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="805" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

805

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC805" class="line" lang="python">            <span class="n" style="color: #333;">priority_gene_trim</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">start_trim1</span><span class="p">,</span> <span class="n" style="color: #333;">end_trim1</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="757" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="806" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

806

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC806" class="line" lang="python">            <span class="n" style="color: #333;">secondary_gene_trim</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">start_trim2</span><span class="p">,</span> <span class="n" style="color: #333;">end_trim2</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="757" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

757

</td>

<td class="new_line diff-line-num" data-linenumber="807" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

807

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC807" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="758" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

758

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<td class="new_line diff-line-num" data-linenumber="808" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

808

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC808" class="line" lang="python">            <span class="n" style="color: #333;">priority_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hmmer_match_details2</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="759" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

759

</td>

<td class="new_line diff-line-num" data-linenumber="809" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

809

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC809" class="line" lang="python">            <span class="n" style="color: #333;">secondary_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hmmer_match_details1</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="760" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

760

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<td class="new_line diff-line-num old" data-linenumber="810" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC760" class="line" lang="python">            <span class="n" style="color: #333;">priority_exons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exons2</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="761" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

761

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<td class="new_line diff-line-num old" data-linenumber="810" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC761" class="line" lang="python">            <span class="n" style="color: #333;">secondary_exons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exons1</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="762" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="810" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

810

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC810" class="line" lang="python">            <span class="n" style="color: #333;">priority_exons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exons2</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">.</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">sort_values</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">by</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"Low coord"</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">ascending</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">strand2</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">==</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"+"</span></span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">)</span></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="762" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="811" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

811

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC811" class="line" lang="python">            <span class="n" style="color: #333;">secondary_exons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exons1</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">.</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">sort_values</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">by</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"Low coord"</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">ascending</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">strand1</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">==</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="s" style="color: #d14;"><span class="idiff addition" style="background-color: #c7f0d2;">"+"</span></span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">)</span></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="762" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

762

</td>

<td class="new_line diff-line-num" data-linenumber="812" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

812

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC812" class="line" lang="python">            <span class="n" style="color: #333;">priority_gene_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_id2</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="763" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

763

</td>

<td class="new_line diff-line-num" data-linenumber="813" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

813

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC813" class="line" lang="python">            <span class="n" style="color: #333;">secondary_gene_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_id1</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="764" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="814" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

814

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC814" class="line" lang="python">            <span class="n" style="color: #333;">priority_gene_trim</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">start_trim2</span><span class="p">,</span> <span class="n" style="color: #333;">end_trim2</span><span class="p">)</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="764" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="815" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

815

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC815" class="line" lang="python">            <span class="n" style="color: #333;">secondary_gene_trim</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">start_trim1</span><span class="p">,</span> <span class="n" style="color: #333;">end_trim1</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="764" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="816" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

816

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC816" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="764" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

764

</td>

<td class="new_line diff-line-num" data-linenumber="817" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

817

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC817" class="line" lang="python">        <span class="n" style="color: #333;">priority_env_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">iter</span><span class="p">(</span><span class="n" style="color: #333;">priority_match</span><span class="p">[</span><span class="n" style="color: #333;">priority_gene_id</span><span class="p">][</span><span class="s" style="color: #d14;">"env_coords"</span><span class="p">])</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="765" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

765

</td>

<td class="new_line diff-line-num" data-linenumber="818" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

818

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC818" class="line" lang="python">        <span class="n" style="color: #333;">secondary_env_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">iter</span><span class="p">(</span><span class="n" style="color: #333;">secondary_match</span><span class="p">[</span><span class="n" style="color: #333;">secondary_gene_id</span><span class="p">][</span><span class="s" style="color: #d14;">"env_coords"</span><span class="p">])</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="766" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

766

</td>

<td class="new_line diff-line-num" data-linenumber="819" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

819

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC819" class="line" lang="python">        <span class="n" style="color: #333;">priority_used_exons</span><span class="p">,</span> <span class="n" style="color: #333;">priority_unused_exons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find_unused_exons</span><span class="p">(</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="767" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

767

</td>

<td class="new_line diff-line-num old" data-linenumber="820" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC767" class="line" lang="python">            <span class="n" style="color: #333;">priority_env_coords</span><span class="p">,</span> <span class="n" style="color: #333;">priority_exons</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="768" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="820" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

820

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC820" class="line" lang="python">            <span class="n" style="color: #333;">priority_env_coords</span><span class="p">,</span> <span class="n" style="color: #333;">priority_exons</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff right addition" style="background-color: #c7f0d2;">priority_gene_trim</span></span></span>

</pre></td>

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768

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<td class="new_line diff-line-num" data-linenumber="821" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

821

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC821" class="line" lang="python">        <span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="769" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

769

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<td class="new_line diff-line-num" data-linenumber="822" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

822

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC822" class="line" lang="python">        <span class="n" style="color: #333;">secondary_used_exons</span><span class="p">,</span> <span class="n" style="color: #333;">secondary_unused_exons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find_unused_exons</span><span class="p">(</span></span>

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<td class="old_line diff-line-num old" data-linenumber="770" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

770

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<td class="new_line diff-line-num old" data-linenumber="823" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC770" class="line" lang="python">            <span class="n" style="color: #333;">secondary_env_coords</span><span class="p">,</span> <span class="n" style="color: #333;">secondary_exons</span></span>

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<td class="old_line diff-line-num new" data-linenumber="771" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="823" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

823

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC823" class="line" lang="python">            <span class="n" style="color: #333;">secondary_env_coords</span><span class="p">,</span> <span class="n" style="color: #333;">secondary_exons</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff right addition" style="background-color: #c7f0d2;">secondary_gene_trim</span></span></span>

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<td class="old_line diff-line-num" data-linenumber="771" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

771

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<td class="new_line diff-line-num" data-linenumber="824" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

824

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC824" class="line" lang="python">        <span class="p">)</span></span>

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772

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<td class="new_line diff-line-num" data-linenumber="825" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

825

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC825" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="773" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

773

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<td class="new_line diff-line-num" data-linenumber="826" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

826

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC826" class="line" lang="python">        <span class="n" style="color: #333;">priority_used_exons</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="844" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="897" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -844,20 +897,25 @@ class GenomeAnalysisEukaryotesMetaeuk(GenomeAnalysisEukaryotes):</td>

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844

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<td class="new_line diff-line-num" data-linenumber="897" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

897

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC897" class="line" lang="python">                        <span class="n" style="color: #333;">overlap</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">match1</span><span class="p">[</span><span class="s" style="color: #d14;">"Score"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">match2</span><span class="p">[</span><span class="s" style="color: #d14;">"Score"</span><span class="p">]</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">overlap</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

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845

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<td class="new_line diff-line-num" data-linenumber="898" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

898

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC898" class="line" lang="python">                    <span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="846" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

846

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<td class="new_line diff-line-num" data-linenumber="899" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

899

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC899" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="847" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

847

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<td class="new_line diff-line-num old" data-linenumber="900" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC847" class="line" lang="python">                <span class="n" style="color: #333;">exons_to_remove</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">secondary_exons</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">index_to_remove</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">secondary_exons</span><span class="p">.</span><span class="n" style="color: #333;">index</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">priority_exons</span></span>

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<td class="old_line diff-line-num new" data-linenumber="848" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="900" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

900

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC900" class="line" lang="python">                <span class="n" style="color: #333;">exons_to_remove</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>

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<td class="old_line diff-line-num new" data-linenumber="848" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="901" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

901

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC901" class="line" lang="python">                    <span class="n" style="color: #333;">secondary_exons</span></span>

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902

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC902" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">index_to_remove</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">secondary_exons</span><span class="p">.</span><span class="n" style="color: #333;">index</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="848" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="903" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

903

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC903" class="line" lang="python">                    <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">priority_exons</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="848" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="904" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

904

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC904" class="line" lang="python">                <span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="848" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

848

</td>

<td class="new_line diff-line-num" data-linenumber="905" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

905

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC905" class="line" lang="python">                <span class="n" style="color: #333;">indices_to_remove</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">extend</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">list</span><span class="p">(</span><span class="n" style="color: #333;">exons_to_remove</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">))</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="849" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

849

</td>

<td class="new_line diff-line-num" data-linenumber="906" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

906

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC906" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">indices_to_remove</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="850" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

850

</td>

<td class="new_line diff-line-num" data-linenumber="907" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

907

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC907" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="851" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

851

</td>

<td class="new_line diff-line-num old" data-linenumber="908" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC851" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">find_unused_exons</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">env_coords</span><span class="p">,</span> <span class="n" style="color: #333;">exons</span><span class="p">):</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="852" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="908" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

908

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC908" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">find_unused_exons</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">env_coords</span><span class="p">,</span> <span class="n" style="color: #333;">exons</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff right addition" style="background-color: #c7f0d2;">gene_trim</span></span><span class="p">):</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="852" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

852

</td>

<td class="new_line diff-line-num" data-linenumber="909" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

909

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC909" class="line" lang="python">        <span class="n" style="color: #333;">remaining_hmm_region</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="853" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

853

</td>

<td class="new_line diff-line-num" data-linenumber="910" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

910

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC910" class="line" lang="python">        <span class="n" style="color: #333;">unused_exons</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="854" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

854

</td>

<td class="new_line diff-line-num" data-linenumber="911" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

911

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC911" class="line" lang="python">        <span class="n" style="color: #333;">used_exons</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="855" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

855

</td>

<td class="new_line diff-line-num" data-linenumber="912" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

912

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC912" class="line" lang="python">        <span class="n" style="color: #333;">hmm_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">next</span><span class="p">(</span><span class="n" style="color: #333;">env_coords</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="856" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="913" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

913

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC913" class="line" lang="python">        <span class="n" style="color: #333;">start_trim</span><span class="p">,</span> <span class="n" style="color: #333;">end_trim</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_trim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">gene_trim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">3</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="856" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

856

</td>

<td class="new_line diff-line-num" data-linenumber="914" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

914

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC914" class="line" lang="python">        <span class="n" style="color: #333;">exon_cumul_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="857" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

857

</td>

<td class="new_line diff-line-num" data-linenumber="915" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

915

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC915" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">entry</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">exons</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">iterrows</span><span class="p">():</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="858" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

858

</td>

<td class="new_line diff-line-num" data-linenumber="916" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

916

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC916" class="line" lang="python">            <span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="s" style="color: #d14;">"index"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">idx</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="859" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

859

</td>

<td class="new_line diff-line-num" data-linenumber="917" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

917

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC917" class="line" lang="python">            <span class="n" style="color: #333;">exon_matched</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="860" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

860

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<td class="new_line diff-line-num old" data-linenumber="918" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC860" class="line" lang="python">            <span class="n" style="color: #333;">exon_size_nt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left deletion" style="background-color: #fac5cd;">Stop</span>"</span><span class="p">])</span> <span class="o" style="font-weight: 600;">-</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff right deletion" style="background-color: #fac5cd;">Start</span>"</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="861" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="918" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

918

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC918" class="line" lang="python">            <span class="n" style="color: #333;">exon_size_nt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left addition" style="background-color: #c7f0d2;">High coord</span>"</span><span class="p">])</span> <span class="o" style="font-weight: 600;">-</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff right addition" style="background-color: #c7f0d2;">Low coord</span>"</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="861" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

861

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<td class="new_line diff-line-num" data-linenumber="919" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

919

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC919" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">exon_size_nt</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="862" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

862

</td>

<td class="new_line diff-line-num" data-linenumber="920" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

920

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC920" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="nc" style="color: #458; font-weight: 600;">BuscoError</span><span class="p">(</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="863" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

863

</td>

<td class="new_line diff-line-num" data-linenumber="921" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

921

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC921" class="line" lang="python">                    <span class="s" style="color: #d14;">"The exon coordinates contain fractional reading frames and are ambiguous."</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="872" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="930" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -872,10 +930,10 @@ class GenomeAnalysisEukaryotesMetaeuk(GenomeAnalysisEukaryotes):</td>

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<td class="old_line diff-line-num" data-linenumber="872" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

872

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<td class="new_line diff-line-num" data-linenumber="930" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

930

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC930" class="line" lang="python">                <span class="n" style="color: #333;">exon_matched</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

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<td class="old_line diff-line-num" data-linenumber="873" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

873

</td>

<td class="new_line diff-line-num" data-linenumber="931" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

931

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC931" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="874" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

874

</td>

<td class="new_line diff-line-num" data-linenumber="932" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

932

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC932" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">hmm_coords</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="875" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

875

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<td class="new_line diff-line-num old" data-linenumber="933" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC875" class="line" lang="python">                <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">hmm_coords</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">exon_cumul_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="876" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="933" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

933

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC933" class="line" lang="python">                <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">hmm_coords</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">-</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">start_trim</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">exon_cumul_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="876" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

876

</td>

<td class="new_line diff-line-num" data-linenumber="934" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

934

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC934" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># hmm starts within exon</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="877" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

877

</td>

<td class="new_line diff-line-num" data-linenumber="935" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

935

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC935" class="line" lang="python">                    <span class="n" style="color: #333;">exon_matched</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="878" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

878

</td>

<td class="new_line diff-line-num old" data-linenumber="936" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC878" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hmm_coords</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_cumul_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="936" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

936

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC936" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hmm_coords</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">-</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">start_trim</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_cumul_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="879" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

879

</td>

<td class="new_line diff-line-num" data-linenumber="937" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

937

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC937" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># hmm ends within exon; cycle to the next hmm region</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="880" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

880

</td>

<td class="new_line diff-line-num" data-linenumber="938" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

938

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC938" class="line" lang="python">                        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="881" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

881

</td>

<td class="new_line diff-line-num" data-linenumber="939" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

939

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC939" class="line" lang="python">                            <span class="n" style="color: #333;">hmm_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">next</span><span class="p">(</span><span class="n" style="color: #333;">env_coords</span><span class="p">)</span></span>

</pre></td>

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<tr class="line_holder match" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="884" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="942" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -884,13 +942,14 @@ class GenomeAnalysisEukaryotesMetaeuk(GenomeAnalysisEukaryotes):</td>

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<td class="old_line diff-line-num" data-linenumber="884" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

884

</td>

<td class="new_line diff-line-num" data-linenumber="942" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

942

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC942" class="line" lang="python">                            <span class="k" style="font-weight: 600;">break</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="885" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

885

</td>

<td class="new_line diff-line-num" data-linenumber="943" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

943

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC943" class="line" lang="python">                        <span class="k" style="font-weight: 600;">continue</span></span>

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<td class="old_line diff-line-num" data-linenumber="886" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

886

</td>

<td class="new_line diff-line-num" data-linenumber="944" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

944

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC944" class="line" lang="python">                    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="887" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

887

</td>

<td class="new_line diff-line-num old" data-linenumber="945" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC887" class="line" lang="python">                        <span class="n" style="color: #333;">remaining_hmm_region</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hmm_coords</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exon_size_aa</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="888" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="945" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

945

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC945" class="line" lang="python">                        <span class="n" style="color: #333;">remaining_hmm_region</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hmm_coords</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;"><span class="idiff left addition" style="background-color: #c7f0d2;">start_trim</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">-</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">exon_size_aa</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>

</pre></td>

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888

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946

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC946" class="line" lang="python">                        <span class="k" style="font-weight: 600;">break</span></span>

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889

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<td class="new_line diff-line-num" data-linenumber="947" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

947

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC947" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">exon_matched</span><span class="p">:</span></span>

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890

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<td class="new_line diff-line-num" data-linenumber="948" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

948

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC948" class="line" lang="python">                <span class="n" style="color: #333;">used_exons</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="891" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

891

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<td class="new_line diff-line-num" data-linenumber="949" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

949

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC949" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="892" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

892

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<td class="new_line diff-line-num" data-linenumber="950" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

950

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC950" class="line" lang="python">                <span class="n" style="color: #333;">unused_exons</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="893" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

893

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<td class="new_line diff-line-num old" data-linenumber="951" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC893" class="line" lang="python">        <span class="n" style="color: #333;">used_exons</span><span class="p">,</span> <span class="n" style="color: #333;">unused_exons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">adjust_exon_categories</span><span class="p">(</span><span class="n" style="color: #333;">used_exons</span><span class="p">,</span> <span class="n" style="color: #333;">unused_exons</span><span class="p">)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="894" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="951" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

951

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC951" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">used_exons</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

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<td class="old_line diff-line-num new" data-linenumber="894" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="952" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

952

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC952" class="line" lang="python">            <span class="n" style="color: #333;">used_exons</span><span class="p">,</span> <span class="n" style="color: #333;">unused_exons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">adjust_exon_categories</span><span class="p">(</span><span class="n" style="color: #333;">used_exons</span><span class="p">,</span> <span class="n" style="color: #333;">unused_exons</span><span class="p">)</span></span>

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894

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953

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC953" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">used_exons</span><span class="p">,</span> <span class="n" style="color: #333;">unused_exons</span></span>

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895

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<td class="new_line diff-line-num" data-linenumber="954" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

954

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC954" class="line" lang="python"></span>

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896

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<td class="new_line diff-line-num" data-linenumber="955" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

955

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC955" class="line" lang="python">    <span class="nd">@staticmethod</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="902" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="961" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -902,16 +961,16 @@ class GenomeAnalysisEukaryotesMetaeuk(GenomeAnalysisEukaryotes):</td>

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902

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<td class="new_line diff-line-num" data-linenumber="961" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC961" class="line" lang="python"><span class="s" style="color: #d14;">        :return:</span></span>

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903

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<td class="new_line diff-line-num" data-linenumber="962" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC962" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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904

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963

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC963" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="905" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

905

</td>

<td class="new_line diff-line-num old" data-linenumber="964" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC905" class="line" lang="python">        <span class="n" style="color: #333;">used_exons_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left right deletion" style="background-color: #fac5cd;">Start</span>"</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">used_exons</span><span class="p">]</span></span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="906" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

906

</td>

<td class="new_line diff-line-num old" data-linenumber="964" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC906" class="line" lang="python">        <span class="n" style="color: #333;">used_exons_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left right deletion" style="background-color: #fac5cd;">Stop</span>"</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">used_exons</span><span class="p">]</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="907" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="964" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

964

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC964" class="line" lang="python">        <span class="n" style="color: #333;">used_exons_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left right addition" style="background-color: #c7f0d2;">Low coord</span>"</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">used_exons</span><span class="p">]</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="907" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="965" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

965

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC965" class="line" lang="python">        <span class="n" style="color: #333;">used_exons_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left right addition" style="background-color: #c7f0d2;">High coord</span>"</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">used_exons</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="907" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

907

</td>

<td class="new_line diff-line-num" data-linenumber="966" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

966

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC966" class="line" lang="python">        <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">min</span><span class="p">(</span><span class="n" style="color: #333;">used_exons_start</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="908" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

908

</td>

<td class="new_line diff-line-num" data-linenumber="967" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

967

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC967" class="line" lang="python">        <span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">max</span><span class="p">(</span><span class="n" style="color: #333;">used_exons_end</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="909" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

909

</td>

<td class="new_line diff-line-num" data-linenumber="968" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

968

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC968" class="line" lang="python">        <span class="n" style="color: #333;">exons_to_remove</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">set</span><span class="p">()</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="910" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

910

</td>

<td class="new_line diff-line-num" data-linenumber="969" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

969

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC969" class="line" lang="python">        <span class="n" style="color: #333;">unused_indices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">exon</span><span class="p">[</span><span class="s" style="color: #d14;">"index"</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">exon</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">unused_exons</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="911" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

911

</td>

<td class="new_line diff-line-num" data-linenumber="970" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

970

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC970" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">exon</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">unused_exons</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="912" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

912

</td>

<td class="new_line diff-line-num" data-linenumber="971" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

971

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC971" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">exon</span><span class="p">[</span><span class="s" style="color: #d14;">"index"</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">exons_to_remove</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="913" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

913

</td>

<td class="new_line diff-line-num old" data-linenumber="972" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC913" class="line" lang="python">                <span class="p">(</span><span class="n" style="color: #333;">exon</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left deletion" style="background-color: #fac5cd;">Start</span>"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">start</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">exon</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff right deletion" style="background-color: #fac5cd;">Start</span>"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="914" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

914

</td>

<td class="new_line diff-line-num old" data-linenumber="972" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC914" class="line" lang="python">                <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="n" style="color: #333;">exon</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left deletion" style="background-color: #fac5cd;">Stop</span>"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">start</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">exon</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff right deletion" style="background-color: #fac5cd;">Stop</span>"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="915" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="972" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

972

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC972" class="line" lang="python">                <span class="p">(</span><span class="n" style="color: #333;">exon</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left addition" style="background-color: #c7f0d2;">Low coord</span>"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">start</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">exon</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff right addition" style="background-color: #c7f0d2;">Low coord</span>"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="915" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="973" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

973

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC973" class="line" lang="python">                <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="n" style="color: #333;">exon</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left addition" style="background-color: #c7f0d2;">High coord</span>"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">start</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">exon</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff right addition" style="background-color: #c7f0d2;">High coord</span>"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="915" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

915

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<td class="new_line diff-line-num" data-linenumber="974" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

974

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC974" class="line" lang="python">            <span class="p">):</span></span>

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<td class="old_line diff-line-num" data-linenumber="916" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

916

</td>

<td class="new_line diff-line-num" data-linenumber="975" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

975

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC975" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># find exons that either start or stop within the "used" range</span></span>

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<td class="old_line diff-line-num" data-linenumber="917" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

917

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<td class="new_line diff-line-num" data-linenumber="976" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

976

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC976" class="line" lang="python">                <span class="n" style="color: #333;">used_exons</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">exon</span><span class="p">)</span></span>

</pre></td>

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<br>

</li>

<li id="ebcdfbf3c61b5f1c742810606673eae398f762bc">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#ebcdfbf3c61b5f1c742810606673eae398f762bc"><strong style="font-weight: bold;">src/busco/analysis/TranscriptomeAnalysis.py</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -6,7 +6,7 @@</td>

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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

6

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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

6

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;">.. versionadded:: 3.0.0</span></span>

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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

7

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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

7

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">.. versionchanged:: 5.4.0</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

8

</td>

<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

8

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

9

</td>

<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right deletion" style="background-color: #fac5cd;">2</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

9

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right addition" style="background-color: #c7f0d2;">3</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

10

</td>

<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

10

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10" class="line" lang="python"><span class="s" style="color: #d14;">Licensed under the MIT license. See LICENSE.md file.</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

11

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

11

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC11" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

12

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

12

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

</pre></td>

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<br>

</li>

<li id="9d54a8efc4f30849596104b53c7b5221e320b1c7">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#9d54a8efc4f30849596104b53c7b5221e320b1c7"><strong style="font-weight: bold;">src/busco/busco_tools/Toolset.py</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -7,7 +7,7 @@</td>

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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">.. versionadded:: 3.0.0</span></span>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="python"><span class="s" style="color: #d14;">.. versionchanged:: 5.4.0</span></span>

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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC9" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right deletion" style="background-color: #fac5cd;">2</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right addition" style="background-color: #c7f0d2;">3</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

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11

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC11" class="line" lang="python"><span class="s" style="color: #d14;">Licensed under the MIT license. See LICENSE.md file.</span></span>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC12" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC13" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

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<li id="44a7a9c3d5eacdcf67af9565b069a28d0ef5092d">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#44a7a9c3d5eacdcf67af9565b069a28d0ef5092d"><strong style="font-weight: bold;">src/busco/busco_tools/base.py</strong></a>

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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -237,6 +237,28 @@ class BaseRunner(Tool, metaclass=ABCMeta):</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC237" class="line" lang="python"></span>

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<td class="new_line diff-line-num" data-linenumber="238" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC238" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span></span>

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<td class="new_line diff-line-num" data-linenumber="239" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC239" class="line" lang="python"></span>

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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC240" class="line" lang="python">    <span class="nd">@staticmethod</span></span>

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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="241" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC241" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_matches</span><span class="p">(</span><span class="n" style="color: #333;">results_grouped</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">):</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC242" class="line" lang="python">        <span class="n" style="color: #333;">g1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results_grouped</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get_group</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="243" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC243" class="line" lang="python">        <span class="n" style="color: #333;">g1_sorted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">sort_values</span><span class="p">(</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="244" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC244" class="line" lang="python">            <span class="s" style="color: #d14;">"Low coord"</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="245" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC245" class="line" lang="python">        <span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># sort to facilitate a single-pass coordinate check</span></span>

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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="246" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC246" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx1</span><span class="p">,</span> <span class="n" style="color: #333;">row1</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">iterrows</span><span class="p">():</span></span>

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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="247" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC247" class="line" lang="python">            <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">idx1</span><span class="p">][</span><span class="s" style="color: #d14;">"Strand"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC248" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="249" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC249" class="line" lang="python">                <span class="n" style="color: #333;">start_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">high_coord</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">idx1</span><span class="p">][</span><span class="s" style="color: #d14;">"High coord"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="250" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC250" class="line" lang="python">                <span class="n" style="color: #333;">stop_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">low_coord</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">idx1</span><span class="p">][</span><span class="s" style="color: #d14;">"Low coord"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="251" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC251" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="252" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC252" class="line" lang="python">                <span class="n" style="color: #333;">start_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">low_coord</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">idx1</span><span class="p">][</span><span class="s" style="color: #d14;">"Low coord"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="253" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC253" class="line" lang="python">                <span class="n" style="color: #333;">stop_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">high_coord</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">idx1</span><span class="p">][</span><span class="s" style="color: #d14;">"High coord"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC254" class="line" lang="python">            <span class="n" style="color: #333;">current_seqid</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{}:{}-{}"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC256" class="line" lang="python">            <span class="p">)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="257" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC257" class="line" lang="python">            <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">[</span><span class="n" style="color: #333;">g1_sorted</span><span class="p">[</span><span class="s" style="color: #d14;">"Low coord"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">low_coord</span><span class="p">].</span><span class="n" style="color: #333;">loc</span><span class="p">[</span></span>

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<td class="new_line diff-line-num new" data-linenumber="258" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC258" class="line" lang="python">                <span class="n" style="color: #333;">g1_sorted</span><span class="p">[</span><span class="s" style="color: #d14;">"Low coord"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">high_coord</span></span>

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<td class="old_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="259" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC259" class="line" lang="python">                <span class="p">]</span>  <span class="c1" style="color: #998; font-style: italic;"># find entries with a start coordinate between the current exon start and end</span></span>

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<td class="new_line diff-line-num new" data-linenumber="260" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC260" class="line" lang="python">            <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">idx1</span><span class="p">,</span> <span class="n" style="color: #333;">current_seqid</span><span class="p">,</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">,</span> <span class="n" style="color: #333;">matches</span></span>

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<td class="new_line diff-line-num new" data-linenumber="261" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC261" class="line" lang="python"></span>

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<td class="new_line diff-line-num" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC262" class="line" lang="python">    <span class="nd">@abstractmethod</span></span>

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<td class="new_line diff-line-num" data-linenumber="263" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC263" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_version</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>

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<td class="new_line diff-line-num" data-linenumber="264" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC264" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span></span>

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<br>

</li>

<li id="a5f82d71f925534007d3cb3b900ad8be00859451">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#a5f82d71f925534007d3cb3b900ad8be00859451"><strong style="font-weight: bold;">src/busco/busco_tools/hmmer.py</strong></a>

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<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -478,19 +478,26 @@ class HMMERRunner(BaseRunner):</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC478" class="line" lang="python">            <span class="n" style="color: #333;">matched_genes_fragment</span><span class="p">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="479" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC479" class="line" lang="python">        <span class="p">)</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC480" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="481" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="481" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC481" class="line" lang="python">    <span class="nd">@staticmethod</span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC482" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_overlaps</span><span class="p">(</span><span class="n" style="color: #333;">matched_records</span><span class="p">):</span></span>

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<td class="new_line diff-line-num new" data-linenumber="481" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

481

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC481" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_overlaps</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">matched_records</span><span class="p">):</span></span>

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483

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<td class="new_line diff-line-num" data-linenumber="482" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

482

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC482" class="line" lang="python">        <span class="n" style="color: #333;">seq_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<td class="old_line diff-line-num old" data-linenumber="484" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

484

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<td class="new_line diff-line-num old" data-linenumber="483" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC484" class="line" lang="python">        <span class="n" style="color: #333;"><span class="idiff left right deletion" style="background-color: #fac5cd;">start</span>_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<td class="old_line diff-line-num old" data-linenumber="485" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

485

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<td class="new_line diff-line-num old" data-linenumber="483" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC485" class="line" lang="python">        <span class="n" style="color: #333;"><span class="idiff left right deletion" style="background-color: #fac5cd;">end</span>_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<td class="old_line diff-line-num new" data-linenumber="486" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="483" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

483

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC483" class="line" lang="python">        <span class="n" style="color: #333;"><span class="idiff left right addition" style="background-color: #c7f0d2;">low</span>_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<td class="old_line diff-line-num new" data-linenumber="486" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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484

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC484" class="line" lang="python">        <span class="n" style="color: #333;"><span class="idiff left right addition" style="background-color: #c7f0d2;">high</span>_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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486

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<td class="new_line diff-line-num" data-linenumber="485" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

485

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC485" class="line" lang="python">        <span class="n" style="color: #333;">scores</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<td class="old_line diff-line-num new" data-linenumber="487" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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486

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC486" class="line" lang="python">        <span class="n" style="color: #333;">strands</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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487

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<td class="new_line diff-line-num" data-linenumber="487" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

487

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC487" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="488" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

488

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<td class="new_line diff-line-num" data-linenumber="488" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

488

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC488" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">matched_records</span><span class="p">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="489" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

489

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<td class="new_line diff-line-num" data-linenumber="489" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

489

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC489" class="line" lang="python">                <span class="n" style="color: #333;">seq_id</span><span class="p">,</span> <span class="n" style="color: #333;">coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="490" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

490

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<td class="new_line diff-line-num old" data-linenumber="490" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC490" class="line" lang="python">                <span class="n" style="color: #333;">start_coord</span><span class="p">,</span> <span class="n" style="color: #333;">end_coord</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">coords</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="491" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="490" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

490

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC490" class="line" lang="python">                <span class="n" style="color: #333;">start_coord</span><span class="p">,</span> <span class="n" style="color: #333;">stop_coord</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">coords</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">))</span></span>

</pre></td>

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491

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC491" class="line" lang="python">                <span class="n" style="color: #333;">low_coord</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">min</span><span class="p">(</span><span class="n" style="color: #333;">start_coord</span><span class="p">,</span> <span class="n" style="color: #333;">stop_coord</span><span class="p">)</span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="492" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

492

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC492" class="line" lang="python">                <span class="n" style="color: #333;">high_coord</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">max</span><span class="p">(</span><span class="n" style="color: #333;">start_coord</span><span class="p">,</span> <span class="n" style="color: #333;">stop_coord</span><span class="p">)</span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="493" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

493

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC493" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">low_coord</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">start_coord</span><span class="p">:</span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="494" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

494

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC494" class="line" lang="python">                    <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"+"</span></span>

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<td class="new_line diff-line-num new" data-linenumber="495" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

495

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC495" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="491" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="496" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

496

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC496" class="line" lang="python">                    <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-"</span></span>

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491

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<td class="new_line diff-line-num" data-linenumber="497" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

497

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC497" class="line" lang="python">                <span class="n" style="color: #333;">seq_ids</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">seq_id</span><span class="p">)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="492" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

492

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<td class="new_line diff-line-num old" data-linenumber="498" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC492" class="line" lang="python">                <span class="n" style="color: #333;">start_coords</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">start_coord</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="493" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

493

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<td class="new_line diff-line-num old" data-linenumber="498" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC493" class="line" lang="python">                <span class="n" style="color: #333;">end_coords</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">end_coord</span><span class="p">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="498" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

498

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC498" class="line" lang="python">                <span class="n" style="color: #333;">low_coords</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">low_coord</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="494" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="499" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

499

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC499" class="line" lang="python">                <span class="n" style="color: #333;">high_coords</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">high_coord</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="494" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="500" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

500

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC500" class="line" lang="python">                <span class="n" style="color: #333;">strands</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">strand</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="494" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

494

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<td class="new_line diff-line-num" data-linenumber="501" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

501

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC501" class="line" lang="python">                <span class="n" style="color: #333;">scores</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">matched_records</span><span class="p">[</span><span class="n" style="color: #333;">record</span><span class="p">][</span><span class="s" style="color: #d14;">"score"</span><span class="p">])</span></span>

</pre></td>

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495

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC502" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span>  <span class="c1" style="color: #998; font-style: italic;"># for protein sequences there is no ":<coords>" suffix, so skip the overlap filtering</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC503" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">matched_records</span></span>

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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -498,45 +505,44 @@ class HMMERRunner(BaseRunner):</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC505" class="line" lang="python">        <span class="n" style="color: #333;">records_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">DataFrame</span><span class="p">(</span></span>

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<td class="new_line diff-line-num" data-linenumber="506" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC506" class="line" lang="python">            <span class="p">{</span></span>

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<td class="new_line diff-line-num" data-linenumber="507" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC507" class="line" lang="python">                <span class="s" style="color: #d14;">"Sequence"</span><span class="p">:</span> <span class="n" style="color: #333;">seq_ids</span><span class="p">,</span></span>

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<td class="new_line diff-line-num old" data-linenumber="508" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC501" class="line" lang="python">                <span class="s" style="color: #d14;">"<span class="idiff left deletion" style="background-color: #fac5cd;">Start"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">:</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff right deletion" style="background-color: #fac5cd;">start</span>_coords</span><span class="p">,</span></span>

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<td class="new_line diff-line-num old" data-linenumber="508" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC502" class="line" lang="python">                <span class="s" style="color: #d14;">"<span class="idiff left deletion" style="background-color: #fac5cd;">Stop"</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">:</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333;"><span class="idiff right deletion" style="background-color: #fac5cd;">end</span>_coords</span><span class="p">,</span></span>

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<td class="new_line diff-line-num new" data-linenumber="508" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC508" class="line" lang="python">                <span class="s" style="color: #d14;">"<span class="idiff left addition" style="background-color: #c7f0d2;">Low coord"</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">:</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff right addition" style="background-color: #c7f0d2;">low</span>_coords</span><span class="p">,</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC509" class="line" lang="python">                <span class="s" style="color: #d14;">"<span class="idiff left addition" style="background-color: #c7f0d2;">High coord"</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">:</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;"><span class="idiff right addition" style="background-color: #c7f0d2;">high</span>_coords</span><span class="p">,</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC510" class="line" lang="python">                <span class="s" style="color: #d14;">"Score"</span><span class="p">:</span> <span class="n" style="color: #333;">scores</span><span class="p">,</span></span>

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<td class="new_line diff-line-num new" data-linenumber="511" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC511" class="line" lang="python">                <span class="s" style="color: #d14;">"Strand"</span><span class="p">:</span> <span class="n" style="color: #333;">strands</span><span class="p">,</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC512" class="line" lang="python">            <span class="p">}</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC513" class="line" lang="python">        <span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="514" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC514" class="line" lang="python">        <span class="n" style="color: #333;">results_grouped</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">records_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">groupby</span><span class="p">(</span><span class="s" style="color: #d14;">"Sequence"</span><span class="p">)</span></span>

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507

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC515" class="line" lang="python">        <span class="n" style="color: #333;">entries_to_remove</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<td class="old_line diff-line-num" data-linenumber="508" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

508

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<td class="new_line diff-line-num" data-linenumber="516" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC516" class="line" lang="python">        <span class="n" style="color: #333;">seq_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results_grouped</span><span class="p">.</span><span class="n" style="color: #333;">groups</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">keys</span><span class="p">()</span></span>

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<td class="old_line diff-line-num" data-linenumber="509" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

509

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<td class="new_line diff-line-num" data-linenumber="517" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC517" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seq_ids</span><span class="p">:</span></span>

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<td class="old_line diff-line-num old" data-linenumber="510" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

510

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<td class="new_line diff-line-num old" data-linenumber="518" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC510" class="line" lang="python">            <span class="n" style="color: #333;">g1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results_grouped</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get_group</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="511" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

511

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<td class="new_line diff-line-num old" data-linenumber="518" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC511" class="line" lang="python">            <span class="n" style="color: #333;">g1_sorted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">sort_values</span><span class="p">(</span></span>

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<td class="old_line diff-line-num old" data-linenumber="512" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

512

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<td class="new_line diff-line-num old" data-linenumber="518" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC512" class="line" lang="python">                <span class="s" style="color: #d14;">"Start"</span></span>

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<td class="old_line diff-line-num old" data-linenumber="513" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

513

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<td class="new_line diff-line-num old" data-linenumber="518" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC513" class="line" lang="python">            <span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># sort to facilitate a single-pass coordinate check</span></span>

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<td class="old_line diff-line-num old" data-linenumber="514" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

514

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<td class="new_line diff-line-num old" data-linenumber="518" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC514" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx1</span><span class="p">,</span> <span class="n" style="color: #333;">row1</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">iterrows</span><span class="p">():</span></span>

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<td class="old_line diff-line-num old" data-linenumber="515" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

515

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<td class="new_line diff-line-num old" data-linenumber="518" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC515" class="line" lang="python">                <span class="n" style="color: #333;">current_record</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">idx1</span><span class="p">]</span></span>

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<td class="old_line diff-line-num old" data-linenumber="516" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

516

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<td class="new_line diff-line-num old" data-linenumber="518" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC516" class="line" lang="python">                <span class="n" style="color: #333;">start_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_record</span><span class="p">[</span><span class="s" style="color: #d14;">"Start"</span><span class="p">]</span></span>

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<td class="old_line diff-line-num old" data-linenumber="517" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

517

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<td class="new_line diff-line-num old" data-linenumber="518" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC517" class="line" lang="python">                <span class="n" style="color: #333;">stop_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_record</span><span class="p">[</span><span class="s" style="color: #d14;">"Stop"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="518" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

518

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<td class="new_line diff-line-num old" data-linenumber="518" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC518" class="line" lang="python">                <span class="n" style="color: #333;">current_seqid</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{}:{}-{}"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>

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<td class="old_line diff-line-num old" data-linenumber="519" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

519

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<td class="new_line diff-line-num old" data-linenumber="518" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC519" class="line" lang="python">                    <span class="n" style="color: #333;">current_record</span><span class="p">[</span><span class="s" style="color: #d14;">"Sequence"</span><span class="p">],</span> <span class="n" style="color: #333;">start_val</span><span class="p">,</span> <span class="n" style="color: #333;">stop_val</span></span>

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<td class="old_line diff-line-num old" data-linenumber="520" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

520

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<td class="new_line diff-line-num old" data-linenumber="518" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC520" class="line" lang="python">                <span class="p">)</span></span>

</pre></td>

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518

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC518" class="line" lang="python">            <span class="n" style="color: #333;">match_finder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get_matches</span><span class="p">(</span><span class="n" style="color: #333;">results_grouped</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="519" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

519

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC519" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">match</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">match_finder</span><span class="p">:</span></span>

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</td>

<td class="new_line diff-line-num new" data-linenumber="520" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

520

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC520" class="line" lang="python">                <span class="n" style="color: #333;">idx1</span><span class="p">,</span> <span class="n" style="color: #333;">current_seqid</span><span class="p">,</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">,</span> <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match</span></span>

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521

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC521" class="line" lang="python">                <span class="nf" style="color: #900; font-weight: 600;">if </span><span class="p">(</span></span>

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522

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<td class="new_line diff-line-num" data-linenumber="522" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

522

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC522" class="line" lang="python">                    <span class="n" style="color: #333;">current_seqid</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">entries_to_remove</span></span>

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523

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<td class="new_line diff-line-num" data-linenumber="523" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC523" class="line" lang="python">                <span class="p">):</span>  <span class="c1" style="color: #998; font-style: italic;"># overlaps with removed entries don't count</span></span>

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<td class="new_line diff-line-num" data-linenumber="524" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC524" class="line" lang="python">                    <span class="k" style="font-weight: 600;">continue</span></span>

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<td class="new_line diff-line-num" data-linenumber="525" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC525" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="526" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

526

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<td class="new_line diff-line-num old" data-linenumber="526" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC526" class="line" lang="python">                <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">[</span><span class="n" style="color: #333;">g1_sorted</span><span class="p">[</span><span class="s" style="color: #d14;">"Start"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">start_val</span><span class="p">].</span><span class="n" style="color: #333;">loc</span><span class="p">[</span></span>

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527

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<td class="new_line diff-line-num old" data-linenumber="526" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC527" class="line" lang="python">                    <span class="n" style="color: #333;">g1_sorted</span><span class="p">[</span><span class="s" style="color: #d14;">"Start"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop_val</span></span>

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528

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<td class="new_line diff-line-num old" data-linenumber="526" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC528" class="line" lang="python">                <span class="p">]</span>  <span class="c1" style="color: #998; font-style: italic;"># find entries with a start coordinate between the current exon start and end</span></span>

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529

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<td class="new_line diff-line-num old" data-linenumber="526" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC529" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">matches</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="530" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

530

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<td class="new_line diff-line-num old" data-linenumber="526" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC530" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">idx1</span><span class="p">][</span><span class="s" style="color: #d14;">"Score"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">idx2</span><span class="p">][</span><span class="s" style="color: #d14;">"Score"</span><span class="p">]:</span></span>

</pre></td>

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526

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC526" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">matches</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># don't consider overlaps with self</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="531" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="527" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

527

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC527" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">idx1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">idx2</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="531" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="528" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

528

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC528" class="line" lang="python">                        <span class="k" style="font-weight: 600;">continue</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="531" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="529" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

529

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC529" class="line" lang="python">                    <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">idx1</span><span class="p">][</span><span class="s" style="color: #d14;">"Score"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">idx2</span><span class="p">][</span><span class="s" style="color: #d14;">"Score"</span><span class="p">]:</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="531" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

531

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<td class="new_line diff-line-num" data-linenumber="530" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

530

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC530" class="line" lang="python">                        <span class="n" style="color: #333;">ind_to_remove</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">idx2</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="532" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

532

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<td class="new_line diff-line-num" data-linenumber="531" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

531

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC531" class="line" lang="python">                    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="533" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

533

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<td class="new_line diff-line-num" data-linenumber="532" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

532

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC532" class="line" lang="python">                        <span class="n" style="color: #333;">ind_to_remove</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">idx1</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="534" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

534

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<td class="new_line diff-line-num" data-linenumber="533" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

533

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC533" class="line" lang="python">                    <span class="n" style="color: #333;">record_to_remove</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">ind_to_remove</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="535" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="534" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

534

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC534" class="line" lang="python">                    <span class="n" style="color: #333;">record_start_coord</span><span class="p">,</span> <span class="n" style="color: #333;">record_stop_coord</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="535" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="535" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

535

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC535" class="line" lang="python">                        <span class="n" style="color: #333;">record_to_remove</span><span class="p">[</span><span class="s" style="color: #d14;">"Low coord"</span><span class="p">],</span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="536" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

536

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC536" class="line" lang="python">                        <span class="n" style="color: #333;">record_to_remove</span><span class="p">[</span><span class="s" style="color: #d14;">"High coord"</span><span class="p">],</span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="537" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

537

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC537" class="line" lang="python">                    <span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">record_to_remove</span><span class="p">[</span><span class="s" style="color: #d14;">"Strand"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"+"</span> <span class="nf" style="color: #900; font-weight: 600;">else </span><span class="p">(</span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="538" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

538

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC538" class="line" lang="python">                        <span class="n" style="color: #333;">record_to_remove</span><span class="p">[</span><span class="s" style="color: #d14;">"High coord"</span><span class="p">],</span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="539" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

539

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC539" class="line" lang="python">                        <span class="n" style="color: #333;">record_to_remove</span><span class="p">[</span><span class="s" style="color: #d14;">"Low coord"</span><span class="p">],</span></span>

</pre></td>

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540

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC540" class="line" lang="python">                    <span class="p">)</span></span>

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535

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<td class="new_line diff-line-num" data-linenumber="541" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

541

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC541" class="line" lang="python">                    <span class="n" style="color: #333;">entries_to_remove</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span></span>

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536

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<td class="new_line diff-line-num" data-linenumber="542" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

542

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC542" class="line" lang="python">                        <span class="s" style="color: #d14;">"{}:{}-{}"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span></span>

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<td class="old_line diff-line-num" data-linenumber="537" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

537

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<td class="new_line diff-line-num" data-linenumber="543" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

543

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC543" class="line" lang="python">                            <span class="n" style="color: #333;">record_to_remove</span><span class="p">[</span><span class="s" style="color: #d14;">"Sequence"</span><span class="p">],</span></span>

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<td class="old_line diff-line-num old" data-linenumber="538" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

538

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<td class="new_line diff-line-num old" data-linenumber="544" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC538" class="line" lang="python">                            <span class="n" style="color: #333;">record_<span class="idiff left deletion" style="background-color: #fac5cd;">to_remove</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">[</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"Start"</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">]</span>,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="539" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

539

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<td class="new_line diff-line-num old" data-linenumber="544" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC539" class="line" lang="python">                            <span class="n" style="color: #333;">record_to<span class="idiff left deletion" style="background-color: #fac5cd;">_remove</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">[</span></span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">"Stop"</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">]</span>,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="540" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="544" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

544

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC544" class="line" lang="python">                            <span class="n" style="color: #333;">record_<span class="idiff left right addition" style="background-color: #c7f0d2;">start_coord</span></span><span class="p">,</span></span>

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545

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC545" class="line" lang="python">                            <span class="n" style="color: #333;">record_<span class="idiff left addition" style="background-color: #c7f0d2;">s</span>to<span class="idiff right addition" style="background-color: #c7f0d2;">p_coord</span></span><span class="p">,</span></span>

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540

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546

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC546" class="line" lang="python">                        <span class="p">)</span></span>

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541

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547

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC547" class="line" lang="python">                    <span class="p">)</span></span>

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542

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548

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC548" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="632" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -632,14 +638,7 @@ class HMMERRunner(BaseRunner):</td>

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632

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638

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC638" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<td class="old_line diff-line-num" data-linenumber="633" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

633

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<td class="new_line diff-line-num" data-linenumber="639" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

639

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC639" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># For a given input dictionary {busco_id: gene_ids}, make sure we are using the corresponding dictionary</span></span>

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634

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<td class="new_line diff-line-num" data-linenumber="640" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

640

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC640" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># {gene_id: busco_matches}</span></span>

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635

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<td class="new_line diff-line-num old" data-linenumber="641" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC635" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">busco_dict</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">is_complete</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

636

</td>

<td class="new_line diff-line-num old" data-linenumber="641" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC636" class="line" lang="python">            <span class="n" style="color: #333;">matched_genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">matched_genes_complete</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="637" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

637

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<td class="new_line diff-line-num old" data-linenumber="641" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC637" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">busco_dict</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">is_very_large</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="638" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

638

</td>

<td class="new_line diff-line-num old" data-linenumber="641" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC638" class="line" lang="python">            <span class="n" style="color: #333;">matched_genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">matched_genes_vlarge</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="639" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

639

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<td class="new_line diff-line-num old" data-linenumber="641" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC639" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">busco_dict</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">is_fragment</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="640" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

640

</td>

<td class="new_line diff-line-num old" data-linenumber="641" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC640" class="line" lang="python">            <span class="n" style="color: #333;">matched_genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">matched_genes_fragment</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="641" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

641

</td>

<td class="new_line diff-line-num old" data-linenumber="641" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC641" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="642" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

642

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<td class="new_line diff-line-num old" data-linenumber="641" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC642" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nc" style="color: #458; font-weight: 600;">BuscoError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unrecognized dictionary of BUSCOs."</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="643" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="641" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

641

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC641" class="line" lang="python">        <span class="n" style="color: #333;">matched_genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get_matched_genes_dict</span><span class="p">(</span><span class="n" style="color: #333;">busco_dict</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="643" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

643

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<td class="new_line diff-line-num" data-linenumber="642" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

642

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC642" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="644" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

644

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<td class="new_line diff-line-num" data-linenumber="643" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

643

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC643" class="line" lang="python">        <span class="n" style="color: #333;">busco_matches_to_remove</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="645" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

645

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<td class="new_line diff-line-num" data-linenumber="644" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

644

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC644" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Keep the best scoring gene if gene is matched by more than one busco with the same match rank</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="679" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="678" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -679,6 +678,17 @@ class HMMERRunner(BaseRunner):</td>

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679

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC678" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="680" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

680

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<td class="new_line diff-line-num" data-linenumber="679" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

679

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC679" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span></span>

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<td class="old_line diff-line-num" data-linenumber="681" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

681

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<td class="new_line diff-line-num" data-linenumber="680" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

680

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC680" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="682" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="681" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

681

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC681" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_matched_genes_dict</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">busco_dict</span><span class="p">):</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="682" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="682" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

682

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC682" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">busco_dict</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">is_complete</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="682" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="683" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

683

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC683" class="line" lang="python">            <span class="n" style="color: #333;">matched_genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">matched_genes_complete</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="682" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="684" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

684

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC684" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">busco_dict</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">is_very_large</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="682" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="685" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

685

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC685" class="line" lang="python">            <span class="n" style="color: #333;">matched_genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">matched_genes_vlarge</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="682" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="686" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

686

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC686" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">busco_dict</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">is_fragment</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="682" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="687" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

687

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC687" class="line" lang="python">            <span class="n" style="color: #333;">matched_genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">matched_genes_fragment</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="682" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="688" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

688

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC688" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="682" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="689" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

689

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC689" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nc" style="color: #458; font-weight: 600;">BuscoError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unrecognized dictionary of BUSCOs."</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="682" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="690" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

690

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC690" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">matched_genes</span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="691" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

691

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC691" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="682" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

682

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<td class="new_line diff-line-num" data-linenumber="692" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

692

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC692" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_remove_low_scoring_matches</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">busco_dict</span><span class="p">):</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="683" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

683

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<td class="new_line diff-line-num" data-linenumber="693" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

693

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC693" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

</pre></td>

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684

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<td class="new_line diff-line-num" data-linenumber="694" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

694

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC694" class="line" lang="python"><span class="s" style="color: #d14;">        Go through input dictionary and remove any gene matches that score less than 85% of the top gene match score</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="689" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="699" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -689,6 +699,8 @@ class HMMERRunner(BaseRunner):</td>

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689

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC699" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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690

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<td class="new_line diff-line-num" data-linenumber="700" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC700" class="line" lang="python">        <span class="n" style="color: #333;">empty_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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691

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<td class="new_line diff-line-num" data-linenumber="701" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC701" class="line" lang="python"></span>

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<td class="old_line diff-line-num new" data-linenumber="692" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="702" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

702

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC702" class="line" lang="python">        <span class="n" style="color: #333;">matched_genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get_matched_genes_dict</span><span class="p">(</span><span class="n" style="color: #333;">busco_dict</span><span class="p">)</span></span>

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703

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC703" class="line" lang="python"></span>

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692

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<td class="new_line diff-line-num" data-linenumber="704" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC704" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># For each busco, keep only matches within 85% of top bitscore match for that busco</span></span>

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693

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<td class="new_line diff-line-num" data-linenumber="705" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC705" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">busco_id</span><span class="p">,</span> <span class="n" style="color: #333;">matches</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">busco_dict</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">items</span><span class="p">():</span></span>

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694

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<td class="new_line diff-line-num" data-linenumber="706" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC706" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">matches</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="714" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="726" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -714,7 +726,9 @@ class HMMERRunner(BaseRunner):</td>

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714

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC726" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">item</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">empty_buscos</span><span class="p">:</span></span>

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<td class="new_line diff-line-num" data-linenumber="727" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC727" class="line" lang="python">            <span class="n" style="color: #333;">busco_id</span><span class="p">,</span> <span class="n" style="color: #333;">gene_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">item</span></span>

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<td class="new_line diff-line-num" data-linenumber="728" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC728" class="line" lang="python">            <span class="n" style="color: #333;">busco_dict</span><span class="p">[</span><span class="n" style="color: #333;">busco_id</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">pop</span><span class="p">(</span><span class="n" style="color: #333;">gene_id</span><span class="p">)</span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC717" class="line" lang="python"></span>

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729

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC729" class="line" lang="python">            <span class="n" style="color: #333;">matched_genes</span><span class="p">[</span><span class="n" style="color: #333;">gene_id</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">remove</span><span class="p">(</span><span class="n" style="color: #333;">busco_id</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="718" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="730" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

730

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC730" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">matched_genes</span><span class="p">[</span><span class="n" style="color: #333;">gene_id</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="718" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="731" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

731

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC731" class="line" lang="python">                <span class="n" style="color: #333;">matched_genes</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">pop</span><span class="p">(</span><span class="n" style="color: #333;">gene_id</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="718" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

718

</td>

<td class="new_line diff-line-num" data-linenumber="732" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

732

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC732" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="719" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

719

</td>

<td class="new_line diff-line-num" data-linenumber="733" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

733

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC733" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="720" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

720

</td>

<td class="new_line diff-line-num" data-linenumber="734" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

734

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC734" class="line" lang="python">    <span class="nd">@staticmethod</span></span>

</pre></td>

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<tr class="line_holder match" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1001" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1015" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -1001,6 +1015,7 @@ class HMMERRunner(BaseRunner):</td>

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<td class="old_line diff-line-num" data-linenumber="1001" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1001

</td>

<td class="new_line diff-line-num" data-linenumber="1015" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1015

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1015" class="line" lang="python">                    <span class="n" style="color: #333;">aa_seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">sequences_aa</span><span class="p">[</span><span class="n" style="color: #333;">gene_id</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">gene_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gene_matches</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1002" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1002

</td>

<td class="new_line diff-line-num" data-linenumber="1016" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1016

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1016" class="line" lang="python">                <span class="k" style="font-weight: 600;">with</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"{}.faa"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">busco</span><span class="p">)),</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f1</span><span class="p">:</span></span>

</pre></td>

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<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1003" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1003

</td>

<td class="new_line diff-line-num" data-linenumber="1017" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1017

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1017" class="line" lang="python">                    <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="n" style="color: #333;">aa_seqs</span><span class="p">,</span> <span class="n" style="color: #333;">f1</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1004" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1018" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1018

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1018" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span></span>

</pre></td>

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<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1004" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1004

</td>

<td class="new_line diff-line-num" data-linenumber="1019" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1019

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1019" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1005" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1005

</td>

<td class="new_line diff-line-num" data-linenumber="1020" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1020

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1020" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_hmmer_results</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">output_lines</span><span class="p">):</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1006" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1006

</td>

<td class="new_line diff-line-num" data-linenumber="1021" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

1021

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1021" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

</pre></td>

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<br>

</li>

<li id="53f20ac1df6a610b6a21de977367ddb3704f3394">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#53f20ac1df6a610b6a21de977367ddb3704f3394"><strong style="font-weight: bold;">src/busco/busco_tools/metaeuk.py</strong></a>

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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -290,8 +290,8 @@ class MetaeukRunner(BaseRunner):</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC290" class="line" lang="python">            <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC291" class="line" lang="python">                <span class="s" style="color: #d14;">"Busco id"</span><span class="p">,</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC292" class="line" lang="python">                <span class="s" style="color: #d14;">"Sequence"</span><span class="p">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="293" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="293" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC293" class="line" lang="python">                <span class="s" style="color: #d14;">"<span class="idiff left right deletion" style="background-color: #fac5cd;">Start</span>"</span><span class="p">,</span></span>

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<td class="new_line diff-line-num old" data-linenumber="293" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC294" class="line" lang="python">                <span class="s" style="color: #d14;">"<span class="idiff left right deletion" style="background-color: #fac5cd;">Stop</span>"</span><span class="p">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="295" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="293" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC293" class="line" lang="python">                <span class="s" style="color: #d14;">"<span class="idiff left right addition" style="background-color: #c7f0d2;">Low coord</span>"</span><span class="p">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="295" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC294" class="line" lang="python">                <span class="s" style="color: #d14;">"<span class="idiff left right addition" style="background-color: #c7f0d2;">High coord</span>"</span><span class="p">,</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC295" class="line" lang="python">                <span class="s" style="color: #d14;">"Strand"</span><span class="p">,</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC296" class="line" lang="python">                <span class="s" style="color: #d14;">"Score"</span><span class="p">,</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC297" class="line" lang="python">                <span class="s" style="color: #d14;">"Run found"</span><span class="p">,</span></span>

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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -302,20 +302,12 @@ class MetaeukRunner(BaseRunner):</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC303" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">results</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC304" class="line" lang="python"></span>

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<td class="new_line diff-line-num old" data-linenumber="305" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC305" class="line" lang="python">    <span class="nd">@staticmethod</span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC306" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">detect_overlap</span><span class="p">(</span><span class="n" style="color: #333;">results_grouped</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">):</span></span>

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<td class="old_line diff-line-num new" data-linenumber="307" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="305" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC305" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">detect_overlap</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">results_grouped</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">):</span></span>

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<td class="old_line diff-line-num" data-linenumber="307" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="306" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC306" class="line" lang="python">        <span class="n" style="color: #333;">overlap_inds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<td class="old_line diff-line-num" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="307" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC307" class="line" lang="python">        <span class="n" style="color: #333;">handled_inds</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">set</span><span class="p">()</span></span>

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<td class="old_line diff-line-num old" data-linenumber="309" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC309" class="line" lang="python">        <span class="n" style="color: #333;">g1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results_grouped</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get_group</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC310" class="line" lang="python">        <span class="n" style="color: #333;">g1_sorted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">sort_values</span><span class="p">(</span></span>

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<td class="old_line diff-line-num old" data-linenumber="311" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC311" class="line" lang="python">            <span class="s" style="color: #d14;">"Start"</span></span>

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<td class="old_line diff-line-num old" data-linenumber="312" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC312" class="line" lang="python">        <span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># sort to facilitate a single-pass coordinate check</span></span>

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<td class="old_line diff-line-num old" data-linenumber="313" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC313" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx1</span><span class="p">,</span> <span class="n" style="color: #333;">row1</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">iterrows</span><span class="p">():</span></span>

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<td class="old_line diff-line-num old" data-linenumber="314" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC314" class="line" lang="python">            <span class="n" style="color: #333;">start_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">idx1</span><span class="p">][</span><span class="s" style="color: #d14;">"Start"</span><span class="p">]</span></span>

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<td class="old_line diff-line-num old" data-linenumber="315" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC315" class="line" lang="python">            <span class="n" style="color: #333;">stop_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">idx1</span><span class="p">][</span><span class="s" style="color: #d14;">"Stop"</span><span class="p">]</span></span>

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<td class="old_line diff-line-num old" data-linenumber="316" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC316" class="line" lang="python">            <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">[</span><span class="n" style="color: #333;">g1_sorted</span><span class="p">[</span><span class="s" style="color: #d14;">"Start"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">start_val</span><span class="p">].</span><span class="n" style="color: #333;">loc</span><span class="p">[</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="317" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC317" class="line" lang="python">                <span class="n" style="color: #333;">g1_sorted</span><span class="p">[</span><span class="s" style="color: #d14;">"Start"</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">stop_val</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="318" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC318" class="line" lang="python">            <span class="p">]</span>  <span class="c1" style="color: #998; font-style: italic;"># find entries with a start coordinate between the current exon start and end</span></span>

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<td class="old_line diff-line-num new" data-linenumber="319" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC308" class="line" lang="python">        <span class="n" style="color: #333;">match_finder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get_matches</span><span class="p">(</span><span class="n" style="color: #333;">results_grouped</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="319" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC309" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">match</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">match_finder</span><span class="p">:</span></span>

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<td class="old_line diff-line-num new" data-linenumber="319" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="310" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC310" class="line" lang="python">            <span class="n" style="color: #333;">idx1</span><span class="p">,</span> <span class="n" style="color: #333;">current_seqid</span><span class="p">,</span> <span class="n" style="color: #333;">g1_sorted</span><span class="p">,</span> <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match</span></span>

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<td class="old_line diff-line-num" data-linenumber="319" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="311" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC311" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">matches</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="320" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="312" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC312" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">idx2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">handled_inds</span><span class="p">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="321" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="313" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC313" class="line" lang="python">                    <span class="k" style="font-weight: 600;">continue</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="340" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="332" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -340,8 +332,8 @@ class MetaeukRunner(BaseRunner):</td>

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<td class="new_line diff-line-num" data-linenumber="332" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC332" class="line" lang="python">                        <span class="p">]</span>  <span class="c1" style="color: #998; font-style: italic;"># check overlaps are on the same strand</span></span>

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<td class="new_line diff-line-num" data-linenumber="333" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC333" class="line" lang="python">                    <span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="334" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC334" class="line" lang="python">                    <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span></span>

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<td class="old_line diff-line-num old" data-linenumber="343" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="335" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC343" class="line" lang="python">                        <span class="n" style="color: #333;">match1_details</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left right deletion" style="background-color: #fac5cd;">Start</span>"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">3</span></span>

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<td class="old_line diff-line-num old" data-linenumber="344" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="335" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC344" class="line" lang="python">                        <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">match2_details</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left right deletion" style="background-color: #fac5cd;">Start</span>"</span><span class="p">]</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="345" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="335" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC335" class="line" lang="python">                        <span class="n" style="color: #333;">match1_details</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left right addition" style="background-color: #c7f0d2;">Low coord</span>"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">3</span></span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC336" class="line" lang="python">                        <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">match2_details</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left right addition" style="background-color: #c7f0d2;">Low coord</span>"</span><span class="p">]</span></span>

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345

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<td class="new_line diff-line-num" data-linenumber="337" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC337" class="line" lang="python">                        <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">3</span>  <span class="c1" style="color: #998; font-style: italic;"># check overlaps are in the same reading frame</span></span>

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346

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<td class="new_line diff-line-num" data-linenumber="338" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

338

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC338" class="line" lang="python">                    <span class="p">)</span></span>

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347

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<td class="new_line diff-line-num" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

339

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC339" class="line" lang="python">                <span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="602" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="594" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -602,6 +594,11 @@ class MetaeukRunner(BaseRunner):</td>

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602

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<td class="new_line diff-line-num" data-linenumber="594" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC594" class="line" lang="python">        <span class="n" style="color: #333;">high_coord</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">header_parts</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">])</span></span>

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<td class="new_line diff-line-num" data-linenumber="595" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC595" class="line" lang="python">        <span class="n" style="color: #333;">exon_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header_parts</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">:]</span></span>

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604

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<td class="new_line diff-line-num" data-linenumber="596" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC596" class="line" lang="python"></span>

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<td class="new_line diff-line-num new" data-linenumber="597" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

597

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC597" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"+"</span><span class="p">:</span></span>

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<td class="new_line diff-line-num new" data-linenumber="598" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

598

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC598" class="line" lang="python">            <span class="n" style="color: #333;">gene_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{}:{}-{}"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">C_acc</span><span class="p">,</span> <span class="n" style="color: #333;">low_coord</span><span class="p">,</span> <span class="n" style="color: #333;">high_coord</span><span class="p">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="599" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

599

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC599" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="new_line diff-line-num new" data-linenumber="600" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

600

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC600" class="line" lang="python">            <span class="n" style="color: #333;">gene_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{}:{}-{}"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">C_acc</span><span class="p">,</span> <span class="n" style="color: #333;">high_coord</span><span class="p">,</span> <span class="n" style="color: #333;">low_coord</span><span class="p">)</span></span>

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601

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC601" class="line" lang="python"></span>

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605

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<td class="new_line diff-line-num" data-linenumber="602" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC602" class="line" lang="python">        <span class="n" style="color: #333;">all_low_exon_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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606

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<td class="new_line diff-line-num" data-linenumber="603" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC603" class="line" lang="python">        <span class="n" style="color: #333;">all_taken_low_exon_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC604" class="line" lang="python">        <span class="n" style="color: #333;">all_high_exon_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="636" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="633" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -636,8 +633,6 @@ class MetaeukRunner(BaseRunner):</td>

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636

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<td class="new_line diff-line-num" data-linenumber="633" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

633

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC633" class="line" lang="python">            <span class="n" style="color: #333;">all_taken_high_exon_coords</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">taken_high_exon_coord</span><span class="p">)</span></span>

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637

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<td class="new_line diff-line-num" data-linenumber="634" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC634" class="line" lang="python">            <span class="n" style="color: #333;">all_taken_exon_nucl_len</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">taken_nucl_len</span><span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="635" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC635" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="639" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

639

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC639" class="line" lang="python">        <span class="n" style="color: #333;">gene_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{}:{}-{}"</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="n" style="color: #333;">C_acc</span><span class="p">,</span> <span class="n" style="color: #333;">low_coord</span><span class="p">,</span> <span class="n" style="color: #333;">high_coord</span><span class="p">)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="640" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

640

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC640" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="641" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

641

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<td class="new_line diff-line-num" data-linenumber="636" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

636

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC636" class="line" lang="python">        <span class="n" style="color: #333;">details</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="642" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

642

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<td class="new_line diff-line-num" data-linenumber="637" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

637

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC637" class="line" lang="python">            <span class="s" style="color: #d14;">"T_acc"</span><span class="p">:</span> <span class="n" style="color: #333;">T_acc</span><span class="p">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="643" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

643

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<td class="new_line diff-line-num" data-linenumber="638" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

638

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC638" class="line" lang="python">            <span class="s" style="color: #d14;">"C_acc"</span><span class="p">:</span> <span class="n" style="color: #333;">C_acc</span><span class="p">,</span></span>

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<br>

</li>

<li id="bd0e703ba072ee7447fcc5bd1e634475b3438cf9">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#bd0e703ba072ee7447fcc5bd1e634475b3438cf9"><strong style="font-weight: bold;">src/busco/run_BUSCO.py</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -13,7 +13,7 @@ To get help, ``busco -h``. See also the user guide.</td>

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13

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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC13" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

14

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14" class="line" lang="python"><span class="s" style="color: #d14;">And visit our website `<http://busco.ezlab.org/>`_</span></span>

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15

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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

16

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<td class="new_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC16" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right deletion" style="background-color: #fac5cd;">2</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC16" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (c) 2016-202<span class="idiff left right addition" style="background-color: #c7f0d2;">3</span>, Evgeny Zdobnov (ez@ezlab.org)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

17

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<td class="new_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

17

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC17" class="line" lang="python"><span class="s" style="color: #d14;">Licensed under the MIT license. See LICENSE.md file.</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

18

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<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

18

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC18" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

19

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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

19

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

</pre></td>

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<br>

</li>

<li id="dba59ea4008347497ea58386e70f0fd75cc9a2e4">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#dba59ea4008347497ea58386e70f0fd75cc9a2e4"><strong style="font-weight: bold;">test_data/bacteria/expected_log.txt</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="old_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1

</td>

<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">2022-12-05 16:29:58 INFO:    ***** Start a BUSCO v5.4.4 analysis, current time: 12/05/2022 16:29:58 *****</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

2

</td>

<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="plaintext">2022-12-05 16:29:58 INFO:    Configuring BUSCO with local environment</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

3

</td>

<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext">2022-12-05 16:29:58 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line.</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

4

</td>

<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="plaintext">2022-12-05 16:29:58 INFO:    Mode is genome</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

5

</td>

<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="plaintext">2022-12-05 16:29:58 INFO:    Downloading information on latest versions of BUSCO data...</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

6

</td>

<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="plaintext">2022-12-05 16:30:00 INFO:    Input file is /busco_wd/test_data/bacteria/genome.fna</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

7

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<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="plaintext">2022-12-05 16:30:00 INFO:    No lineage specified. Running lineage auto selector.</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1" class="line" lang="plaintext">2023-04-28 14:24:43 INFO:    ***** Start a BUSCO v5.4.7 analysis, current time: 04/28/2023 14:24:43 *****</span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2" class="line" lang="plaintext">2023-04-28 14:24:43 INFO:    Configuring BUSCO with local environment</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

3

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="plaintext">2023-04-28 14:24:43 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line.</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

4

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4" class="line" lang="plaintext">2023-04-28 14:24:43 INFO:    Mode is genome</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

5

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="plaintext">2023-04-28 14:24:43 INFO:    'Force' option selected; overwriting previous results directory</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

6

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6" class="line" lang="plaintext">2023-04-28 14:24:44 INFO:    Downloading information on latest versions of BUSCO data...</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

7

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7" class="line" lang="plaintext">2023-04-28 14:24:46 INFO:    Input file is /busco_wd/test_data/bacteria/genome.fna</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

8

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC8" class="line" lang="plaintext">2023-04-28 14:24:46 INFO:    No lineage specified. Running lineage auto selector.</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

8

</td>

<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

9

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC9" class="line" lang="plaintext"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

9

</td>

<td class="new_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:00</span> INFO:  ***** Starting Auto Select Lineage *****</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

10

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:46</span> INFO: ***** Starting Auto Select Lineage *****</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

10

</td>

<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

11

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC11" class="line" lang="plaintext">    This process runs BUSCO on the generic lineage datasets for the domains archaea, bacteria and eukaryota. Once the optimal domain is selected, BUSCO automatically attempts to find the most appropriate BUSCO dataset to use based on phylogenetic placement.</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

11

</td>

<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

12

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC12" class="line" lang="plaintext">    --auto-lineage-euk and --auto-lineage-prok are also available if you know your input assembly is, or is not, an eukaryote. See the user guide for more information.</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

12

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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

13

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC13" class="line" lang="plaintext">    A reminder: Busco evaluations are valid when an appropriate dataset is used, i.e., the dataset belongs to the lineage of the species to test. Because of overlapping markers/spurious matches among domains, busco matches in another domain do not necessarily mean that your genome/proteome contains sequences from this domain. However, a high busco score in multiple domains might help you identify possible contaminations.</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

13

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<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC13" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:00</span> INFO: Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

14

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<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:30:00</span> INFO:       Running 1 job(s) on bbtools, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05</span>/202<span class="idiff deletion" style="background-color: #fac5cd;">2</span> 1<span class="idiff right deletion" style="background-color: #fac5cd;">6:30:00</span></span>

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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC15" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:02</span> INFO: [bbtools]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC16" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:02</span> INFO: ***** Run Prodigal on input to predict and extract genes *****</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC17" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:02</span> INFO: Running Prodigal with genetic code 11 in single mode</span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

18

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC18" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:30:02</span> INFO:       Running 1 job(s) on prodigal, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05</span>/202<span class="idiff deletion" style="background-color: #fac5cd;">2</span> 1<span class="idiff right deletion" style="background-color: #fac5cd;">6:30:02</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

19

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC19" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:04</span> INFO: [prodigal]      1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

20

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC20" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:04</span> INFO: Genetic code 11 selected as optimal</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

21

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC21" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:04</span> INFO: ***** Run HMMER on gene sequences *****</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

22

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC22" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:30:04</span> INFO:       Running 194 job(s) on hmmsearch, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05</span>/202<span class="idiff deletion" style="background-color: #fac5cd;">2</span> 1<span class="idiff right deletion" style="background-color: #fac5cd;">6:30:04</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

23

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC23" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:06</span> INFO: [hmmsearch]     20 of 194 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

24

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC24" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:06</span> INFO: [hmmsearch]     39 of 194 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

25

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC25" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:06</span> INFO: [hmmsearch]     59 of 194 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

26

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC26" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:06</span> INFO: [hmmsearch]     78 of 194 task(s) completed</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

27

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC27" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:06</span> INFO: [hmmsearch]     97 of 194 task(s) completed</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

28

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC28" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:07</span> INFO: [hmmsearch]     117 of 194 task(s) completed</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

29

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC29" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:07</span> INFO: [hmmsearch]     136 of 194 task(s) completed</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

30

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC30" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:07</span> INFO: [hmmsearch]     156 of 194 task(s) completed</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

31

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC31" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:07</span> INFO: [hmmsearch]     175 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

32

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC32" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:07</span> INFO: [hmmsearch]     194 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

33

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC33" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:09</span> INFO: Results:        C:5.2%[S:5.2%,D:0.0%],F:1.5%,M:93.3%,n:194         </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

14

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:46</span> INFO: Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

15

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC15" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:24:46</span> INFO:       Running 1 job(s) on bbtools, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28</span>/202<span class="idiff addition" style="background-color: #c7f0d2;">3</span> 1<span class="idiff right addition" style="background-color: #c7f0d2;">4:24:46</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

16

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC16" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:48</span> INFO: [bbtools]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

17

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC17" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:48</span> INFO: ***** Run Prodigal on input to predict and extract genes *****</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

18

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC18" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:48</span> INFO: Running Prodigal with genetic code 11 in single mode</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

19

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC19" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:24:48</span> INFO:       Running 1 job(s) on prodigal, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28</span>/202<span class="idiff addition" style="background-color: #c7f0d2;">3</span> 1<span class="idiff right addition" style="background-color: #c7f0d2;">4:24:48</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

20

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC20" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:50</span> INFO: [prodigal]      1 of 1 task(s) completed</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

21

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC21" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:50</span> INFO: Genetic code 11 selected as optimal</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

22

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC22" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:50</span> INFO: ***** Run HMMER on gene sequences *****</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

23

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:24:50</span> INFO:       Running 194 job(s) on hmmsearch, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28</span>/202<span class="idiff addition" style="background-color: #c7f0d2;">3</span> 1<span class="idiff right addition" style="background-color: #c7f0d2;">4:24:50</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

24

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC24" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:51</span> INFO: [hmmsearch]     20 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

25

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC25" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:52</span> INFO: [hmmsearch]     39 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

26

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC26" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:52</span> INFO: [hmmsearch]     59 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

27

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC27" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:52</span> INFO: [hmmsearch]     78 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

28

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC28" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:52</span> INFO: [hmmsearch]     97 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

29

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC29" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:52</span> INFO: [hmmsearch]     117 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

30

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC30" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:52</span> INFO: [hmmsearch]     136 of 194 task(s) completed</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

31

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC31" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:52</span> INFO: [hmmsearch]     156 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

32

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC32" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:53</span> INFO: [hmmsearch]     175 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

33

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC33" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:53</span> INFO: [hmmsearch]     194 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

34

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC34" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:54</span> INFO: Results:        C:5.2%[S:5.2%,D:0.0%],F:1.5%,M:93.3%,n:194         </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

34

</td>

<td class="new_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

35

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC35" class="line" lang="plaintext"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

35

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC35" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:09</span> INFO: Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2020-03-06)</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

36

</td>

<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC36" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:30:09</span> INFO:       Running 1 job(s) on bbtools, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05</span>/202<span class="idiff deletion" style="background-color: #fac5cd;">2</span> 1<span class="idiff right deletion" style="background-color: #fac5cd;">6:30:09</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="37" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

37

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC37" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:11</span> INFO: [bbtools]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

38

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC38" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:11</span> INFO: ***** Run Prodigal on input to predict and extract genes *****</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="39" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

39

</td>

<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC39" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:11</span> INFO: Genetic code 11 selected as optimal</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

40

</td>

<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC40" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:11</span> INFO: ***** Run HMMER on gene sequences *****</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="41" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

41

</td>

<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC41" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:30:11</span> INFO:       Running 124 job(s) on hmmsearch, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05</span>/202<span class="idiff deletion" style="background-color: #fac5cd;">2</span> 1<span class="idiff right deletion" style="background-color: #fac5cd;">6:30:11</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

42

</td>

<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC42" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:12</span> INFO: [hmmsearch]     13 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

43

</td>

<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC43" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:13</span> INFO: [hmmsearch]     25 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

44

</td>

<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC44" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:13</span> INFO: [hmmsearch]     38 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="45" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

45

</td>

<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC45" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:13</span> INFO: [hmmsearch]     50 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

46

</td>

<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC46" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:13</span> INFO: [hmmsearch]     63 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

47

</td>

<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC47" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:13</span> INFO: [hmmsearch]     75 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

48

</td>

<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC48" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:13</span> INFO: [hmmsearch]     87 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

49

</td>

<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC49" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:13</span> INFO: [hmmsearch]     100 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="50" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

50

</td>

<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC50" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:14</span> INFO: [hmmsearch]     112 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="51" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

51

</td>

<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC51" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:14</span> INFO: [hmmsearch]     124 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="52" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

52

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC52" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:16</span> INFO: Results:        C:21.0%[S:21.0%,D:0.0%],F:0.8%,M:78.2%,n:124       </span>

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<td class="old_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC36" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:55</span> INFO: Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2020-03-06)</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC37" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:24:55</span> INFO:       Running 1 job(s) on bbtools, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28</span>/202<span class="idiff addition" style="background-color: #c7f0d2;">3</span> 1<span class="idiff right addition" style="background-color: #c7f0d2;">4:24:55</span></span>

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<td class="old_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

38

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC38" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:57</span> INFO: [bbtools]       1 of 1 task(s) completed</span>

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<td class="old_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

39

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC39" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:57</span> INFO: ***** Run Prodigal on input to predict and extract genes *****</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

40

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC40" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:58</span> INFO: Genetic code 11 selected as optimal</span>

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<td class="old_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

41

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC41" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:58</span> INFO: ***** Run HMMER on gene sequences *****</span>

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<td class="old_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

42

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC42" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:24:58</span> INFO:       Running 124 job(s) on hmmsearch, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28</span>/202<span class="idiff addition" style="background-color: #c7f0d2;">3</span> 1<span class="idiff right addition" style="background-color: #c7f0d2;">4:24:58</span></span>

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<td class="old_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

43

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC43" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:24:59</span> INFO: [hmmsearch]     13 of 124 task(s) completed</span>

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<td class="old_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC44" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:00</span> INFO: [hmmsearch]     25 of 124 task(s) completed</span>

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<td class="old_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC45" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:00</span> INFO: [hmmsearch]     38 of 124 task(s) completed</span>

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<td class="old_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC46" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:00</span> INFO: [hmmsearch]     50 of 124 task(s) completed</span>

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<td class="old_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC47" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:00</span> INFO: [hmmsearch]     63 of 124 task(s) completed</span>

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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC48" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:00</span> INFO: [hmmsearch]     75 of 124 task(s) completed</span>

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<td class="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC49" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:00</span> INFO: [hmmsearch]     87 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

50

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC50" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:00</span> INFO: [hmmsearch]     100 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

51

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC51" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:01</span> INFO: [hmmsearch]     112 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

52

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC52" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:01</span> INFO: [hmmsearch]     124 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

53

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC53" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:03</span> INFO: Results:        C:21.0%[S:21.0%,D:0.0%],F:0.8%,M:78.2%,n:124       </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

53

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<td class="new_line diff-line-num" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

54

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC54" class="line" lang="plaintext"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

54

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC54" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:17</span> INFO: Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2020-09-10)</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

55

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC55" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:30:17</span> INFO:       Running 1 job(s) on bbtools, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05</span>/202<span class="idiff deletion" style="background-color: #fac5cd;">2</span> 1<span class="idiff right deletion" style="background-color: #fac5cd;">6:30:17</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="56" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

56

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC56" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:30:19</span> INFO: [bbtools]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="57" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

57

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC57" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:30:19</span> INFO:       Running 1 job(s) on metaeuk, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05</span>/202<span class="idiff deletion" style="background-color: #fac5cd;">2</span> 1<span class="idiff right deletion" style="background-color: #fac5cd;">6:30:19</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="58" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

58

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC58" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:31:01</span> INFO: [metaeuk]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="59" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

59

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC59" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:31:02</span> INFO: ***** Run HMMER on gene sequences *****</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="60" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

60

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC60" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:31:02</span> INFO:       Running 255 job(s) on hmmsearch, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05</span>/202<span class="idiff deletion" style="background-color: #fac5cd;">2</span> 1<span class="idiff right deletion" style="background-color: #fac5cd;">6:31:02</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="61" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

61

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC61" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:31:03</span> INFO: [hmmsearch]     26 of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="62" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

62

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC62" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:31:04</span> INFO: [hmmsearch]     51 of 255 task(s) completed</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="63" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

63

</td>

<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC63" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:31:04</span> INFO: [hmmsearch]     77 of 255 task(s) completed</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="64" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

64

</td>

<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC64" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:31:04</span> INFO: [hmmsearch]     102 of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="65" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

65

</td>

<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC65" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:31:05</span> INFO: [hmmsearch]     128 of 255 task(s) completed</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="66" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

66

</td>

<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC66" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:31:05</span> INFO: [hmmsearch]     153 of 255 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="67" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

67

</td>

<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC67" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:31:05</span> INFO: [hmmsearch]     179 of 255 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

68

</td>

<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC68" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:31:05</span> INFO: [hmmsearch]     204 of 255 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

69

</td>

<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC69" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:31:06</span> INFO: [hmmsearch]     230 of 255 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

70

</td>

<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC70" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:31:06</span> INFO: [hmmsearch]     255 of 255 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="71" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

71

</td>

<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC71" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:31:08</span> INFO: Validating exons and removing overlapping matches</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="72" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

72

</td>

<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC72" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:31:10</span> INFO: 0 candidate overlapping regions found</span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

73

</td>

<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC73" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:31:10</span> INFO: 3 exons in total</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

74

</td>

<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC74" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:31:10</span> INFO: Results:        C:1.2%[S:1.2%,D:0.0%],F:0.0%,M:98.8%,n:255         </span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

55

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC55" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:03</span> INFO: Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2020-09-10)</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

56

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC56" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:25:03</span> INFO:       Running 1 job(s) on bbtools, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28</span>/202<span class="idiff addition" style="background-color: #c7f0d2;">3</span> 1<span class="idiff right addition" style="background-color: #c7f0d2;">4:25:03</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

57

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC57" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:06</span> INFO: [bbtools]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

58

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC58" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:25:06</span> INFO:       Running 1 job(s) on metaeuk, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28</span>/202<span class="idiff addition" style="background-color: #c7f0d2;">3</span> 1<span class="idiff right addition" style="background-color: #c7f0d2;">4:25:06</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

59

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC59" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:49</span> INFO: [metaeuk]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

60

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC60" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:50</span> INFO: ***** Run HMMER on gene sequences *****</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

61

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC61" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:25:50</span> INFO:       Running 255 job(s) on hmmsearch, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28</span>/202<span class="idiff addition" style="background-color: #c7f0d2;">3</span> 1<span class="idiff right addition" style="background-color: #c7f0d2;">4:25:50</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

62

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC62" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:52</span> INFO: [hmmsearch]     26 of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

63

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC63" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:52</span> INFO: [hmmsearch]     51 of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

64

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC64" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:52</span> INFO: [hmmsearch]     77 of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

65

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC65" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:52</span> INFO: [hmmsearch]     102 of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

66

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC66" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:52</span> INFO: [hmmsearch]     128 of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

67

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC67" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:52</span> INFO: [hmmsearch]     153 of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

68

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC68" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:52</span> INFO: [hmmsearch]     179 of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

69

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC69" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:53</span> INFO: [hmmsearch]     204 of 255 task(s) completed</span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

70

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC70" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:53</span> INFO: [hmmsearch]     230 of 255 task(s) completed</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

71

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC71" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:53</span> INFO: [hmmsearch]     255 of 255 task(s) completed</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

72

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC72" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:55</span> INFO: Validating exons and removing overlapping matches</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

73

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC73" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:55</span> INFO: 0 candidate overlapping regions found</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

74

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC74" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:55</span> INFO: 3 exons in total</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

75

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC75" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:25:55</span> INFO: Results:        C:1.2%[S:1.2%,D:0.0%],F:0.0%,M:98.8%,n:255         </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

75

</td>

<td class="new_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

76

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC76" class="line" lang="plaintext"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

76

</td>

<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC76" class="line" lang="plaintext">2022-12-05 16:31:10 INFO:   Extracting missing and fragmented buscos from the file refseq_db.faa...</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

77

</td>

<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC77" class="line" lang="plaintext">2022-12-05 16:31:26 INFO:   Running 1 job(s) on metaeuk, starting at 12/05/2022 16:31:26</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="78" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

78

</td>

<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC78" class="line" lang="plaintext">2022-12-05 16:32:23 INFO:   [metaeuk]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="79" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

79

</td>

<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC79" class="line" lang="plaintext">2022-12-05 16:32:24 INFO:   ***** Run HMMER on gene sequences *****</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="80" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

80

</td>

<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC80" class="line" lang="plaintext">2022-12-05 16:32:24 INFO:   Running 252 job(s) on hmmsearch, starting at 12/05/2022 16:32:24</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="81" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

81

</td>

<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC81" class="line" lang="plaintext">2022-12-05 16:32:26 INFO:   [hmmsearch]     26 of 252 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="82" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

82

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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC82" class="line" lang="plaintext">2022-12-05 16:32:26 INFO:   [hmmsearch]     51 of 252 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="83" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

83

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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC83" class="line" lang="plaintext">2022-12-05 16:32:26 INFO:   [hmmsearch]     76 of 252 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

84

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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC84" class="line" lang="plaintext">2022-12-05 16:32:26 INFO:   [hmmsearch]     101 of 252 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="85" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

85

</td>

<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC85" class="line" lang="plaintext">2022-12-05 16:32:27 INFO:   [hmmsearch]     126 of 252 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

86

</td>

<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC86" class="line" lang="plaintext">2022-12-05 16:32:27 INFO:   [hmmsearch]     152 of 252 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="87" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

87

</td>

<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC87" class="line" lang="plaintext">2022-12-05 16:32:27 INFO:   [hmmsearch]     177 of 252 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="88" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

88

</td>

<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC88" class="line" lang="plaintext">2022-12-05 16:32:27 INFO:   [hmmsearch]     202 of 252 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="89" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

89

</td>

<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC89" class="line" lang="plaintext">2022-12-05 16:32:27 INFO:   [hmmsearch]     227 of 252 task(s) completed</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="90" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

90

</td>

<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC90" class="line" lang="plaintext">2022-12-05 16:32:27 INFO:   [hmmsearch]     252 of 252 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

91

</td>

<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC91" class="line" lang="plaintext">2022-12-05 16:32:29 INFO:   Validating exons and removing overlapping matches</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

92

</td>

<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC92" class="line" lang="plaintext">2022-12-05 16:32:30 INFO:   0 candidate overlapping regions found</span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="93" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

93

</td>

<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC93" class="line" lang="plaintext">2022-12-05 16:32:30 INFO:   3 exons in total</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="94" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

94

</td>

<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC94" class="line" lang="plaintext">2022-12-05 16:32:30 INFO:   Results:        C:1.2%[S:1.2%,D:0.0%],F:0.0%,M:98.8%,n:255         </span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

77

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC77" class="line" lang="plaintext">2023-04-28 14:25:55 INFO:   Extracting missing and fragmented buscos from the file refseq_db.faa...</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

78

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC78" class="line" lang="plaintext">2023-04-28 14:26:13 INFO:   Running 1 job(s) on metaeuk, starting at 04/28/2023 14:26:13</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

79

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC79" class="line" lang="plaintext">2023-04-28 14:27:12 INFO:   [metaeuk]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

80

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC80" class="line" lang="plaintext">2023-04-28 14:27:13 INFO:   ***** Run HMMER on gene sequences *****</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

81

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC81" class="line" lang="plaintext">2023-04-28 14:27:13 INFO:   Running 252 job(s) on hmmsearch, starting at 04/28/2023 14:27:13</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="82" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

82

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC82" class="line" lang="plaintext">2023-04-28 14:27:15 INFO:   [hmmsearch]     26 of 252 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

83

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC83" class="line" lang="plaintext">2023-04-28 14:27:15 INFO:   [hmmsearch]     51 of 252 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

84

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC84" class="line" lang="plaintext">2023-04-28 14:27:15 INFO:   [hmmsearch]     76 of 252 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

85

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC85" class="line" lang="plaintext">2023-04-28 14:27:15 INFO:   [hmmsearch]     101 of 252 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

86

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC86" class="line" lang="plaintext">2023-04-28 14:27:15 INFO:   [hmmsearch]     126 of 252 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

87

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC87" class="line" lang="plaintext">2023-04-28 14:27:15 INFO:   [hmmsearch]     152 of 252 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

88

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC88" class="line" lang="plaintext">2023-04-28 14:27:15 INFO:   [hmmsearch]     177 of 252 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

89

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC89" class="line" lang="plaintext">2023-04-28 14:27:16 INFO:   [hmmsearch]     202 of 252 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

90

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC90" class="line" lang="plaintext">2023-04-28 14:27:16 INFO:   [hmmsearch]     202 of 252 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

91

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC91" class="line" lang="plaintext">2023-04-28 14:27:16 INFO:   [hmmsearch]     227 of 252 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

92

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC92" class="line" lang="plaintext">2023-04-28 14:27:16 INFO:   [hmmsearch]     252 of 252 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

93

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC93" class="line" lang="plaintext">2023-04-28 14:27:17 INFO:   Validating exons and removing overlapping matches</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

94

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC94" class="line" lang="plaintext">2023-04-28 14:27:18 INFO:   0 candidate overlapping regions found</span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

95

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC95" class="line" lang="plaintext">2023-04-28 14:27:18 INFO:   3 exons in total</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

96

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC96" class="line" lang="plaintext">2023-04-28 14:27:18 INFO:   Results:        C:1.2%[S:1.2%,D:0.0%],F:0.0%,M:98.8%,n:255         </span>

</pre></td>

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95

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<td class="new_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

97

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC97" class="line" lang="plaintext"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

96

</td>

<td class="new_line diff-line-num old" data-linenumber="98" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC96" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:32:30</span> INFO: bacteria_odb10 selected</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="97" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

98

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC98" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:27:18</span> INFO: bacteria_odb10 selected</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

97

</td>

<td class="new_line diff-line-num" data-linenumber="99" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

99

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC99" class="line" lang="plaintext"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="98" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

98

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC98" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:32:30</span> INFO: ***** Searching tree for chosen lineage to find best taxonomic match *****</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

100

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC100" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:27:18</span> INFO:        ***** Searching tree for chosen lineage to find best taxonomic match *****</span>

</pre></td>

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99

</td>

<td class="new_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

101

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC101" class="line" lang="plaintext"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

100

</td>

<td class="new_line diff-line-num old" data-linenumber="102" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC100" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:32:30</span> INFO:        Extract markers...</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

101

</td>

<td class="new_line diff-line-num old" data-linenumber="102" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC101" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:32:30</span> INFO:        Place the markers on the reference tree...</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="102" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

102

</td>

<td class="new_line diff-line-num old" data-linenumber="102" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC102" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:32:30</span> INFO:      Running 1 job(s) on sepp, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05</span>/202<span class="idiff deletion" style="background-color: #fac5cd;">2</span> 1<span class="idiff right deletion" style="background-color: #fac5cd;">6:32:30</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="103" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

103

</td>

<td class="new_line diff-line-num old" data-linenumber="102" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC103" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:33:54</span> INFO:        [sepp]  1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="104" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

104

</td>

<td class="new_line diff-line-num old" data-linenumber="102" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC104" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:33:54</span> INFO:        Not enough markers were placed on the tree (11). Root lineage bacteria is kept</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="105" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

105

</td>

<td class="new_line diff-line-num old" data-linenumber="102" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC105" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:33:54</span> INFO:        </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

102

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC102" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:27:18</span> INFO:        Extract markers...</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

103

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC103" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:27:18</span> INFO:        Place the markers on the reference tree...</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

104

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC104" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:27:18</span> INFO:      Running 1 job(s) on sepp, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28</span>/202<span class="idiff addition" style="background-color: #c7f0d2;">3</span> 1<span class="idiff right addition" style="background-color: #c7f0d2;">4:27:18</span></span>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="105" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

105

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC105" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:28:48</span> INFO:        [sepp]  1 of 1 task(s) completed</span>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

106

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC106" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:28:48</span> INFO:        Not enough markers were placed on the tree (11). Root lineage bacteria is kept</span>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

107

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC107" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:28:48</span> INFO:        </span>

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106

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<td class="new_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC108" class="line" lang="plaintext"></span>

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107

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<td class="new_line diff-line-num" data-linenumber="109" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC109" class="line" lang="plaintext">   --------------------------------------------------</span>

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<td class="old_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="110" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC110" class="line" lang="plaintext">   |Results from dataset bacteria_odb10              |</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="117" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -115,12 +117,12 @@</td>

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<td class="new_line diff-line-num" data-linenumber="117" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC117" class="line" lang="plaintext">   |97     Missing BUSCOs (M)                        |</span>

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<td class="old_line diff-line-num" data-linenumber="116" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="118" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC118" class="line" lang="plaintext">   |124    Total BUSCO groups searched               |</span>

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<td class="old_line diff-line-num" data-linenumber="117" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

117

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<td class="new_line diff-line-num" data-linenumber="119" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC119" class="line" lang="plaintext">   --------------------------------------------------</span>

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<td class="old_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

118

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<td class="new_line diff-line-num old" data-linenumber="120" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC118" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:33:54</span> INFO:      BUSCO analysis done with WARNING(s). Total running time: 2<span class="idiff right deletion" style="background-color: #fac5cd;">3</span>4 seconds</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC120" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:28:48</span> INFO:      BUSCO analysis done with WARNING(s). Total running time: 24<span class="idiff right addition" style="background-color: #c7f0d2;">3</span> seconds</span>

</pre></td>

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<td class="new_line diff-line-num" data-linenumber="121" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC121" class="line" lang="plaintext"></span>

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120

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<td class="new_line diff-line-num" data-linenumber="122" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC122" class="line" lang="plaintext">***** Summary of warnings: *****</span>

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<td class="new_line diff-line-num old" data-linenumber="123" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC121" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:2<span class="idiff right deletion" style="background-color: #fac5cd;">9:58</span> WARNING:busco.BuscoConfig      Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line.</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

123

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC123" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:2<span class="idiff right addition" style="background-color: #c7f0d2;">4:43</span> WARNING:busco.BuscoConfig      Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line.</span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="122" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

122

</td>

<td class="new_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

124

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC124" class="line" lang="plaintext"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="123" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

123

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<td class="new_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC123" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:33:54</span> INFO:        Results written in /busco_wd/test_bacteria</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="124" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

124

</td>

<td class="new_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC124" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:33:54</span> INFO:        For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

125

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC125" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:28:48</span> INFO:        Results written in /busco_wd/test_bacteria</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

126

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC126" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:28:48</span> INFO:        For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html</span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

125

</td>

<td class="new_line diff-line-num" data-linenumber="127" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

127

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC127" class="line" lang="plaintext"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

126

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<td class="new_line diff-line-num old" data-linenumber="128" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC126" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:33:54</span> INFO:        Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO</span></pre></td>

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<td class="old_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

128

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC128" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:28:48</span> INFO:        Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO</span></pre></td>

</tr>

</table>

<br>

</li>

<li id="11a346fb4c4f7cb01e1e5466e6712687c54fe746">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#11a346fb4c4f7cb01e1e5466e6712687c54fe746"><strong style="font-weight: bold;">test_data/eukaryota/expected_log.txt</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="old_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

1

</td>

<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">2022-12-05 16:33:55 INFO:    ***** Start a BUSCO v5.4.4 analysis, current time: 12/05/2022 16:33:55 *****</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

2

</td>

<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="plaintext">2022-12-05 16:33:55 INFO:    Configuring BUSCO with local environment</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

3

</td>

<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext">2022-12-05 16:33:55 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line.</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

4

</td>

<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="plaintext">2022-12-05 16:33:55 INFO:    Mode is genome</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

5

</td>

<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="plaintext">2022-12-05 16:33:55 INFO:    Downloading information on latest versions of BUSCO data...</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

6

</td>

<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="plaintext">2022-12-05 16:33:57 INFO:    Input file is /busco_wd/test_data/eukaryota/genome.fna</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

7

</td>

<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="plaintext">2022-12-05 16:33:57 INFO:    No lineage specified. Running lineage auto selector.</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

1

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1" class="line" lang="plaintext">2023-04-28 14:28:49 INFO:    ***** Start a BUSCO v5.4.7 analysis, current time: 04/28/2023 14:28:49 *****</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

2

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2" class="line" lang="plaintext">2023-04-28 14:28:49 INFO:    Configuring BUSCO with local environment</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

3

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="plaintext">2023-04-28 14:28:49 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line.</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

4

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4" class="line" lang="plaintext">2023-04-28 14:28:49 INFO:    Mode is genome</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

5

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="plaintext">2023-04-28 14:28:49 INFO:    'Force' option selected; overwriting previous results directory</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

6

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6" class="line" lang="plaintext">2023-04-28 14:28:50 INFO:    Downloading information on latest versions of BUSCO data...</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

7

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7" class="line" lang="plaintext">2023-04-28 14:28:52 INFO:    Input file is /busco_wd/test_data/eukaryota/genome.fna</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

8

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC8" class="line" lang="plaintext">2023-04-28 14:28:52 INFO:    No lineage specified. Running lineage auto selector.</span>

</pre></td>

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<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

8

</td>

<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

9

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC9" class="line" lang="plaintext"></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

9

</td>

<td class="new_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:33</span>:5<span class="idiff right deletion" style="background-color: #fac5cd;">7</span> INFO:   ***** Starting Auto Select Lineage *****</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

10

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:28</span>:5<span class="idiff right addition" style="background-color: #c7f0d2;">2</span> INFO:  ***** Starting Auto Select Lineage *****</span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

10

</td>

<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

11

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC11" class="line" lang="plaintext">    This process runs BUSCO on the generic lineage datasets for the domains archaea, bacteria and eukaryota. Once the optimal domain is selected, BUSCO automatically attempts to find the most appropriate BUSCO dataset to use based on phylogenetic placement.</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

11

</td>

<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

12

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC12" class="line" lang="plaintext">    --auto-lineage-euk and --auto-lineage-prok are also available if you know your input assembly is, or is not, an eukaryote. See the user guide for more information.</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

12

</td>

<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

13

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC13" class="line" lang="plaintext">    A reminder: Busco evaluations are valid when an appropriate dataset is used, i.e., the dataset belongs to the lineage of the species to test. Because of overlapping markers/spurious matches among domains, busco matches in another domain do not necessarily mean that your genome/proteome contains sequences from this domain. However, a high busco score in multiple domains might help you identify possible contaminations.</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

13

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC13" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:33</span>:5<span class="idiff right deletion" style="background-color: #fac5cd;">7</span> INFO:  Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

14

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:33</span>:5<span class="idiff deletion" style="background-color: #fac5cd;">7</span> INFO:        Running 1 job(s) on bbtools, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05</span>/202<span class="idiff deletion" style="background-color: #fac5cd;">2</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6:33</span>:5<span class="idiff right deletion" style="background-color: #fac5cd;">7</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

15

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC15" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:33</span>:5<span class="idiff right deletion" style="background-color: #fac5cd;">8</span> INFO:  [bbtools]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

16

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<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC16" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:33</span>:5<span class="idiff right deletion" style="background-color: #fac5cd;">8</span> INFO:  ***** Run Prodigal on input to predict and extract genes *****</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

17

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC17" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:33</span>:5<span class="idiff right deletion" style="background-color: #fac5cd;">8</span> INFO:  Running Prodigal with genetic code 11 in single mode</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

18

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<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC18" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:33</span>:5<span class="idiff deletion" style="background-color: #fac5cd;">8</span> INFO:        Running 1 job(s) on prodigal, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05</span>/202<span class="idiff deletion" style="background-color: #fac5cd;">2</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6:33</span>:5<span class="idiff right deletion" style="background-color: #fac5cd;">8</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

19

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<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC19" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:33</span>:5<span class="idiff right deletion" style="background-color: #fac5cd;">9</span> INFO:  [prodigal]      1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

20

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC20" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:33</span>:5<span class="idiff right deletion" style="background-color: #fac5cd;">9</span> INFO:  Genetic code 11 selected as optimal</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

21

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<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC21" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:33</span>:5<span class="idiff right deletion" style="background-color: #fac5cd;">9</span> INFO:  ***** Run HMMER on gene sequences *****</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

22

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<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC22" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:33</span>:5<span class="idiff deletion" style="background-color: #fac5cd;">9</span> INFO:        Running 194 job(s) on hmmsearch, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05</span>/202<span class="idiff deletion" style="background-color: #fac5cd;">2</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6:33</span>:5<span class="idiff right deletion" style="background-color: #fac5cd;">9</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

23

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<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC23" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:34:00</span> INFO: [hmmsearch]     20 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

24

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<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC24" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:34:00</span> INFO: [hmmsearch]     39 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

25

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC25" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:34:00</span> INFO: [hmmsearch]     59 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

26

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC26" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:34:00</span> INFO: [hmmsearch]     78 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

27

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC27" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:34:00</span> INFO: [hmmsearch]     97 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

28

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC28" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:34:01</span> INFO: [hmmsearch]     117 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

29

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC29" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:34:01</span> INFO: [hmmsearch]     136 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

30

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC30" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:34:01</span> INFO: [hmmsearch]     156 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

31

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC31" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:34:01</span> INFO: [hmmsearch]     175 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

32

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC32" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:34:01</span> INFO: [hmmsearch]     194 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

33

</td>

<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC33" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:34</span>:0<span class="idiff right deletion" style="background-color: #fac5cd;">2</span> INFO:  Results:        C:1.0%[S:1.0%,D:0.0%],F:0.5%,M:98.5%,n:194         </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

14

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:28</span>:5<span class="idiff right addition" style="background-color: #c7f0d2;">2</span> INFO:  Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

15

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC15" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:28</span>:5<span class="idiff addition" style="background-color: #c7f0d2;">2</span> INFO:        Running 1 job(s) on bbtools, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28</span>/202<span class="idiff addition" style="background-color: #c7f0d2;">3</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4:28</span>:5<span class="idiff right addition" style="background-color: #c7f0d2;">2</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

16

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC16" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:28</span>:5<span class="idiff right addition" style="background-color: #c7f0d2;">3</span> INFO:  [bbtools]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

17

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC17" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:28</span>:5<span class="idiff right addition" style="background-color: #c7f0d2;">3</span> INFO:  ***** Run Prodigal on input to predict and extract genes *****</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

18

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC18" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:28</span>:5<span class="idiff right addition" style="background-color: #c7f0d2;">3</span> INFO:  Running Prodigal with genetic code 11 in single mode</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

19

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC19" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:28</span>:5<span class="idiff addition" style="background-color: #c7f0d2;">3</span> INFO:        Running 1 job(s) on prodigal, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28</span>/202<span class="idiff addition" style="background-color: #c7f0d2;">3</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4:28</span>:5<span class="idiff right addition" style="background-color: #c7f0d2;">3</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

20

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC20" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:28</span>:5<span class="idiff right addition" style="background-color: #c7f0d2;">4</span> INFO:  [prodigal]      1 of 1 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

21

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC21" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:28</span>:5<span class="idiff right addition" style="background-color: #c7f0d2;">4</span> INFO:  Genetic code 11 selected as optimal</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

22

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC22" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:28</span>:5<span class="idiff right addition" style="background-color: #c7f0d2;">4</span> INFO:  ***** Run HMMER on gene sequences *****</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

23

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:28</span>:5<span class="idiff addition" style="background-color: #c7f0d2;">4</span> INFO:        Running 194 job(s) on hmmsearch, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28</span>/202<span class="idiff addition" style="background-color: #c7f0d2;">3</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4:28</span>:5<span class="idiff right addition" style="background-color: #c7f0d2;">4</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

24

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC24" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:28:56</span> INFO: [hmmsearch]     20 of 194 task(s) completed</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

25

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC25" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:28:56</span> INFO: [hmmsearch]     39 of 194 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

26

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC26" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:28:56</span> INFO: [hmmsearch]     59 of 194 task(s) completed</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

27

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC27" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:28:57</span> INFO: [hmmsearch]     78 of 194 task(s) completed</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

28

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC28" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:28:57</span> INFO: [hmmsearch]     97 of 194 task(s) completed</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

29

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC29" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:28:57</span> INFO: [hmmsearch]     117 of 194 task(s) completed</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

30

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC30" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:28:57</span> INFO: [hmmsearch]     136 of 194 task(s) completed</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

31

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC31" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:28:57</span> INFO: [hmmsearch]     156 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC32" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:28:57</span> INFO: [hmmsearch]     175 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

33

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC33" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:28:57</span> INFO: [hmmsearch]     194 of 194 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

34

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC34" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:29</span>:0<span class="idiff right addition" style="background-color: #c7f0d2;">0</span> INFO:  Results:        C:1.0%[S:1.0%,D:0.0%],F:0.5%,M:98.5%,n:194         </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

34

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<td class="new_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

35

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC35" class="line" lang="plaintext"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

35

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC35" class="line" lang="plaintext">2022-12-05 16:34:02 INFO:   Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2020-03-06)</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

36

</td>

<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC36" class="line" lang="plaintext">2022-12-05 16:34:02 INFO:   Running 1 job(s) on bbtools, starting at 12/05/2022 16:34:02</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="37" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

37

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC37" class="line" lang="plaintext">2022-12-05 16:34:03 INFO:   [bbtools]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

38

</td>

<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC38" class="line" lang="plaintext">2022-12-05 16:34:03 INFO:   ***** Run Prodigal on input to predict and extract genes *****</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="39" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

39

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC39" class="line" lang="plaintext">2022-12-05 16:34:03 INFO:   Genetic code 11 selected as optimal</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

40

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC40" class="line" lang="plaintext">2022-12-05 16:34:03 INFO:   ***** Run HMMER on gene sequences *****</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="41" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

41

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC41" class="line" lang="plaintext">2022-12-05 16:34:03 INFO:   Running 124 job(s) on hmmsearch, starting at 12/05/2022 16:34:03</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

42

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC42" class="line" lang="plaintext">2022-12-05 16:34:04 INFO:   [hmmsearch]     13 of 124 task(s) completed</span>

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<td class="old_line diff-line-num old" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

43

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC43" class="line" lang="plaintext">2022-12-05 16:34:04 INFO:   [hmmsearch]     25 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

44

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC44" class="line" lang="plaintext">2022-12-05 16:34:04 INFO:   [hmmsearch]     38 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="45" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

45

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC45" class="line" lang="plaintext">2022-12-05 16:34:04 INFO:   [hmmsearch]     50 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

46

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC46" class="line" lang="plaintext">2022-12-05 16:34:04 INFO:   [hmmsearch]     63 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

47

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC47" class="line" lang="plaintext">2022-12-05 16:34:04 INFO:   [hmmsearch]     75 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

48

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC48" class="line" lang="plaintext">2022-12-05 16:34:04 INFO:   [hmmsearch]     87 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

49

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC49" class="line" lang="plaintext">2022-12-05 16:34:04 INFO:   [hmmsearch]     100 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="50" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

50

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC50" class="line" lang="plaintext">2022-12-05 16:34:04 INFO:   [hmmsearch]     112 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="51" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

51

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC51" class="line" lang="plaintext">2022-12-05 16:34:04 INFO:   [hmmsearch]     124 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="52" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

52

</td>

<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC52" class="line" lang="plaintext">2022-12-05 16:34:05 WARNING:        BUSCO did not find any match. Make sure to check the log files if this is unexpected.</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

53

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC53" class="line" lang="plaintext">2022-12-05 16:34:05 INFO:   Results:        C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:124        </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

36

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC36" class="line" lang="plaintext">2023-04-28 14:29:00 INFO:   Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2020-03-06)</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

37

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC37" class="line" lang="plaintext">2023-04-28 14:29:00 INFO:   Running 1 job(s) on bbtools, starting at 04/28/2023 14:29:00</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

38

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC38" class="line" lang="plaintext">2023-04-28 14:29:02 INFO:   [bbtools]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

39

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC39" class="line" lang="plaintext">2023-04-28 14:29:02 INFO:   ***** Run Prodigal on input to predict and extract genes *****</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

40

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC40" class="line" lang="plaintext">2023-04-28 14:29:02 INFO:   Genetic code 11 selected as optimal</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

41

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC41" class="line" lang="plaintext">2023-04-28 14:29:02 INFO:   ***** Run HMMER on gene sequences *****</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

42

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC42" class="line" lang="plaintext">2023-04-28 14:29:02 INFO:   Running 124 job(s) on hmmsearch, starting at 04/28/2023 14:29:02</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC43" class="line" lang="plaintext">2023-04-28 14:29:03 INFO:   [hmmsearch]     13 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

44

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC44" class="line" lang="plaintext">2023-04-28 14:29:03 INFO:   [hmmsearch]     25 of 124 task(s) completed</span>

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<td class="old_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

45

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC45" class="line" lang="plaintext">2023-04-28 14:29:03 INFO:   [hmmsearch]     50 of 124 task(s) completed</span>

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<td class="old_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

46

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC46" class="line" lang="plaintext">2023-04-28 14:29:03 INFO:   [hmmsearch]     63 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

47

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC47" class="line" lang="plaintext">2023-04-28 14:29:03 INFO:   [hmmsearch]     75 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

48

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC48" class="line" lang="plaintext">2023-04-28 14:29:03 INFO:   [hmmsearch]     87 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

49

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC49" class="line" lang="plaintext">2023-04-28 14:29:03 INFO:   [hmmsearch]     100 of 124 task(s) completed</span>

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</td>

<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

50

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC50" class="line" lang="plaintext">2023-04-28 14:29:03 INFO:   [hmmsearch]     112 of 124 task(s) completed</span>

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<td class="old_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

51

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC51" class="line" lang="plaintext">2023-04-28 14:29:03 INFO:   [hmmsearch]     124 of 124 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

52

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC52" class="line" lang="plaintext">2023-04-28 14:29:05 WARNING:        BUSCO did not find any match. Make sure to check the log files if this is unexpected.</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

53

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC53" class="line" lang="plaintext">2023-04-28 14:29:05 INFO:   Results:        C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:124        </span>

</pre></td>

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54

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<td class="new_line diff-line-num" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

54

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC54" class="line" lang="plaintext"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

55

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC55" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:34</span>:05 INFO: Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2020-09-10)</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="56" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

56

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC56" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:34</span>:05 INFO:       Running 1 job(s) on bbtools, starting at <span class="idiff right deletion" style="background-color: #fac5cd;">12/05/2022 16:34</span>:05</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="57" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC57" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:34</span>:0<span class="idiff right deletion" style="background-color: #fac5cd;">6</span> INFO:  [bbtools]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="58" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC58" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:34</span>:0<span class="idiff deletion" style="background-color: #fac5cd;">6</span> INFO:        Running 1 job(s) on metaeuk, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05</span>/202<span class="idiff deletion" style="background-color: #fac5cd;">2</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6:34</span>:0<span class="idiff right deletion" style="background-color: #fac5cd;">6</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="59" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

59

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC59" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:34:35</span> INFO: [metaeuk]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="60" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

60

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC60" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:34:37</span> INFO: ***** Run HMMER on gene sequences *****</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="61" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

61

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC61" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:34:37</span> INFO:       Running 255 job(s) on hmmsearch, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05</span>/202<span class="idiff deletion" style="background-color: #fac5cd;">2</span> 1<span class="idiff right deletion" style="background-color: #fac5cd;">6:34:37</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="62" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC62" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:34:38</span> INFO:       [hmmsearch]     <span class="idiff right deletion" style="background-color: #fac5cd;">26</span> of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="63" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC63" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:34:38</span> INFO:       [hmmsearch]     <span class="idiff right deletion" style="background-color: #fac5cd;">51</span> of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="64" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC64" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:34:39</span> INFO:       [hmmsearch]     <span class="idiff right deletion" style="background-color: #fac5cd;">77</span> of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="65" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

65

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC65" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:34:39</span> INFO:       [hmmsearch]     1<span class="idiff right deletion" style="background-color: #fac5cd;">0</span>2 of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="66" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

66

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC66" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:34:39</span> INFO:       [hmmsearch]     1<span class="idiff right deletion" style="background-color: #fac5cd;">28</span> of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="67" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

67

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC67" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:34:39</span> INFO:       [hmmsearch]     1<span class="idiff right deletion" style="background-color: #fac5cd;">53</span> of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

68

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC68" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:34:39</span> INFO:       [hmmsearch]     <span class="idiff right deletion" style="background-color: #fac5cd;">179</span> of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

69

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC69" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:34:39</span> INFO:       [hmmsearch]     20<span class="idiff right deletion" style="background-color: #fac5cd;">4</span> of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

70

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC70" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:34:40</span> INFO: [hmmsearch]     255 of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="71" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC71" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:34:41</span> INFO: Validating exons and removing overlapping matches</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="72" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

72

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC72" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:34:42</span> INFO: 0 candidate overlapping regions found</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

73

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC73" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:34:42</span> INFO: 51 exons in total</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

74

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<td class="new_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC74" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:34:42</span> INFO: Results:        C:19.2%[S:19.2%,D:0.0%],F:0.8%,M:80.0%,n:255       </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

55

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC55" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:29</span>:05 INFO: Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2020-09-10)</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

56

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC56" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:29</span>:05 INFO:       Running 1 job(s) on bbtools, starting at <span class="idiff right addition" style="background-color: #c7f0d2;">04/28/2023 14:29</span>:05</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

57

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC57" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:29</span>:0<span class="idiff right addition" style="background-color: #c7f0d2;">7</span> INFO:  [bbtools]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

58

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC58" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:29</span>:0<span class="idiff addition" style="background-color: #c7f0d2;">7</span> INFO:        Running 1 job(s) on metaeuk, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28</span>/202<span class="idiff addition" style="background-color: #c7f0d2;">3</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4:29</span>:0<span class="idiff right addition" style="background-color: #c7f0d2;">7</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

59

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC59" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:29:49</span> INFO: [metaeuk]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

60

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC60" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:29:51</span> INFO: ***** Run HMMER on gene sequences *****</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

61

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC61" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:29:51</span> INFO:       Running 255 job(s) on hmmsearch, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28</span>/202<span class="idiff addition" style="background-color: #c7f0d2;">3</span> 1<span class="idiff right addition" style="background-color: #c7f0d2;">4:29:51</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

62

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC62" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:29:52</span> INFO:       [hmmsearch]     <span class="idiff right addition" style="background-color: #c7f0d2;">51</span> of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

63

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC63" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:29:53</span> INFO:       [hmmsearch]     <span class="idiff right addition" style="background-color: #c7f0d2;">77</span> of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

64

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC64" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:29:53</span> INFO:       [hmmsearch]     <span class="idiff right addition" style="background-color: #c7f0d2;">102</span> of 255 task(s) completed</span>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

65

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC65" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:29:53</span> INFO:       [hmmsearch]     12<span class="idiff right addition" style="background-color: #c7f0d2;">8</span> of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

66

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC66" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:29:53</span> INFO:       [hmmsearch]     1<span class="idiff right addition" style="background-color: #c7f0d2;">53</span> of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

67

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC67" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:29:53</span> INFO:       [hmmsearch]     1<span class="idiff right addition" style="background-color: #c7f0d2;">79</span> of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

68

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC68" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:29:53</span> INFO:       [hmmsearch]     <span class="idiff right addition" style="background-color: #c7f0d2;">204</span> of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

69

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC69" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:29:54</span> INFO:       [hmmsearch]     2<span class="idiff right addition" style="background-color: #c7f0d2;">3</span>0 of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

70

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC70" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:29:54</span> INFO: [hmmsearch]     255 of 255 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

71

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC71" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:29:56</span> INFO: Validating exons and removing overlapping matches</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

72

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC72" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:29:57</span> INFO: 0 candidate overlapping regions found</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

73

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC73" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:29:57</span> INFO: 51 exons in total</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

74

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC74" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:29:57</span> INFO: Results:        C:19.2%[S:19.2%,D:0.0%],F:0.8%,M:80.0%,n:255       </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

75

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<td class="new_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

75

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC75" class="line" lang="plaintext"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

76

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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC76" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:34:42</span> INFO: Extracting missing and fragmented buscos from the file refseq_db.faa...</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

77

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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC77" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff deletion" style="background-color: #fac5cd;">4:57</span> INFO: Running 1 job(s) on metaeuk, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05</span>/202<span class="idiff deletion" style="background-color: #fac5cd;">2</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">4:57</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="78" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

78

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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC78" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:17</span> INFO:   [metaeuk]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="79" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

79

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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC79" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:1</span>8 INFO:   ***** Run HMMER on gene sequences *****</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="80" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC80" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff deletion" style="background-color: #fac5cd;">5:1</span>8 INFO: Running 206 job(s) on hmmsearch, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05/2022</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:1</span>8</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="81" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

81

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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC81" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:2</span>0 INFO:   [hmmsearch]     21 of 206 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="82" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

82

</td>

<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC82" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:2</span>0 INFO:   [hmmsearch]     42 of 206 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="83" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

83

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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC83" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:2</span>0 INFO:   [hmmsearch]     62 of 206 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

84

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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC84" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:20</span> INFO:   [hmmsearch]     83 of 206 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="85" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

85

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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC85" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:20</span> INFO:   [hmmsearch]     104 of 206 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

86

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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC86" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:20</span> INFO:   [hmmsearch]     124 of 206 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="87" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

87

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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC87" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:20</span> INFO:   [hmmsearch]     145 of 206 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="88" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

88

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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC88" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:20</span> INFO:   [hmmsearch]     165 of 206 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="89" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

89

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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC89" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:20</span> INFO:   [hmmsearch]     186 of 206 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="90" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC90" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:20</span> INFO:   [hmmsearch]     206 of 206 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

91

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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC91" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:22</span> INFO:   Validating exons and removing overlapping matches</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC92" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:23</span> INFO:   0 candidate overlapping regions found</span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="93" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

93

</td>

<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC93" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:23</span> INFO:   51 exons in total</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="94" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

94

</td>

<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC94" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:23</span> INFO:   Results:        C:19.2%[S:19.2%,D:0.0%],F:0.8%,M:80.0%,n:255       </span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

76

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC76" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:29:57</span> INFO: Extracting missing and fragmented buscos from the file refseq_db.faa...</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

77

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC77" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff addition" style="background-color: #c7f0d2;">0:14</span> INFO: Running 1 job(s) on metaeuk, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28</span>/202<span class="idiff addition" style="background-color: #c7f0d2;">3</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:14</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

78

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC78" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:45</span> INFO:   [metaeuk]       1 of 1 task(s) completed</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

79

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC79" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:4</span>8 INFO:   ***** Run HMMER on gene sequences *****</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

80

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC80" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff addition" style="background-color: #c7f0d2;">0:4</span>8 INFO: Running 206 job(s) on hmmsearch, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28/2023</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:4</span>8</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

81

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC81" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:5</span>0 INFO:   [hmmsearch]     21 of 206 task(s) completed</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="82" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

82

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC82" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:5</span>0 INFO:   [hmmsearch]     42 of 206 task(s) completed</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

83

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC83" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:5</span>0 INFO:   [hmmsearch]     62 of 206 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

84

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC84" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:51</span> INFO:   [hmmsearch]     83 of 206 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

85

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC85" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:51</span> INFO:   [hmmsearch]     104 of 206 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

86

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC86" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:51</span> INFO:   [hmmsearch]     124 of 206 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

87

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC87" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:51</span> INFO:   [hmmsearch]     145 of 206 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

88

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC88" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:51</span> INFO:   [hmmsearch]     165 of 206 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

89

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC89" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:51</span> INFO:   [hmmsearch]     186 of 206 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

90

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC90" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:52</span> INFO:   [hmmsearch]     206 of 206 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

91

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC91" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:54</span> INFO:   Validating exons and removing overlapping matches</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

92

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC92" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:56</span> INFO:   0 candidate overlapping regions found</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

93

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC93" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:56</span> INFO:   51 exons in total</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

94

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC94" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:56</span> INFO:   Results:        C:19.2%[S:19.2%,D:0.0%],F:0.8%,M:80.0%,n:255       </span>

</pre></td>

</tr>

<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

95

</td>

<td class="new_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

95

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC95" class="line" lang="plaintext"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

96

</td>

<td class="new_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC96" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:23</span> INFO:   eukaryota_odb10 selected</span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="97" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

96

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC96" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:56</span> INFO:   eukaryota_odb10 selected</span>

</pre></td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

97

</td>

<td class="new_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

97

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC97" class="line" lang="plaintext"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="98" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

98

</td>

<td class="new_line diff-line-num old" data-linenumber="98" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC98" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:23</span> INFO:   ***** Searching tree for chosen lineage to find best taxonomic match *****</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

98

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC98" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:56</span> INFO:   ***** Searching tree for chosen lineage to find best taxonomic match *****</span>

</pre></td>

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<tr class="line_holder" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="99" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

99

</td>

<td class="new_line diff-line-num" data-linenumber="99" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

99

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC99" class="line" lang="plaintext"></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

100

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC100" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:23</span> INFO:  Extract markers...</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

101

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC101" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:23</span> INFO:  Place the markers on the reference tree...</span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="102" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

102

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC102" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff deletion" style="background-color: #fac5cd;">5:23</span> INFO:        Running 1 job(s) on sepp, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05</span>/202<span class="idiff deletion" style="background-color: #fac5cd;">2</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">5:23</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="103" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

103

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC103" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">8:57</span> INFO:  [sepp]  1 of 1 task(s) completed</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="104" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

104

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC104" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">8:58</span> INFO:  Lineage saccharomycetes is selected, supported by 18 markers out of 19</span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="105" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

105

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC105" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">8:58</span> INFO:  Running BUSCO using lineage dataset saccharomycetes_odb10 (eukaryota, 2020-08-05)</span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

106

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC106" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff deletion" style="background-color: #fac5cd;">8:58</span> INFO:        Running 1 job(s) on bbtools, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05</span>/202<span class="idiff deletion" style="background-color: #fac5cd;">2</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">8:58</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="107" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

107

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC107" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">8:59</span> INFO:  [bbtools]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="108" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

108

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<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC108" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff deletion" style="background-color: #fac5cd;">8:59</span> INFO:        Running 1 job(s) on metaeuk, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05</span>/202<span class="idiff deletion" style="background-color: #fac5cd;">2</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">8:59</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

109

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC109" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">9:06</span> INFO:  [metaeuk]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="110" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

110

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<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC110" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">9:07</span> INFO:  ***** Run HMMER on gene sequences *****</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="111" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

111

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<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC111" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff deletion" style="background-color: #fac5cd;">9:07</span> INFO:        Running 2137 job(s) on hmmsearch, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05</span>/202<span class="idiff deletion" style="background-color: #fac5cd;">2</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">9:07</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="112" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

112

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC112" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff deletion" style="background-color: #fac5cd;">9</span>:1<span class="idiff right deletion" style="background-color: #fac5cd;">2</span> INFO:   [hmmsearch]     214 of 2137 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

113

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC113" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">9:14</span> INFO:  [hmmsearch]     428 of 2137 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="114" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

114

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC114" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">9:16</span> INFO:  [hmmsearch]     642 of 2137 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="115" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

115

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC115" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">9:18</span> INFO:  [hmmsearch]     855 of 2137 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="116" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

116

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC116" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff deletion" style="background-color: #fac5cd;">9</span>:2<span class="idiff right deletion" style="background-color: #fac5cd;">0</span> INFO:   [hmmsearch]     1069 of 2137 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="117" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

117

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC117" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff deletion" style="background-color: #fac5cd;">9</span>:2<span class="idiff right deletion" style="background-color: #fac5cd;">2</span> INFO:   [hmmsearch]     1283 of 2137 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

118

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<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC118" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">9:23</span> INFO:  [hmmsearch]     1496 of 2137 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="119" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

119

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC119" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">9:25</span> INFO:  [hmmsearch]     1710 of 2137 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="120" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

120

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC120" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">9:27</span> INFO:  [hmmsearch]     1924 of 2137 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="121" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

121

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<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC121" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff deletion" style="background-color: #fac5cd;">9</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">1</span> INFO:   [hmmsearch]     2137 of 2137 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

122

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<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC122" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">9:34</span> INFO:  Validating exons and removing overlapping matches</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="123" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

123

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<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC123" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">9:36</span> INFO:  0 candidate overlapping regions found</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="124" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

124

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC124" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">9:36</span> INFO:  45 exons in total</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

125

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC125" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">9:36</span> INFO:  Extracting missing and fragmented buscos from the file refseq_db.faa...</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

126

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC126" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff deletion" style="background-color: #fac5cd;">9:41</span> INFO:        Running 1 job(s) on metaeuk, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05</span>/202<span class="idiff deletion" style="background-color: #fac5cd;">2</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">9:41</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="127" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

127

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<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC127" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">9:48</span> INFO:  [metaeuk]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="128" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

128

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC128" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff deletion" style="background-color: #fac5cd;">9</span>:5<span class="idiff right deletion" style="background-color: #fac5cd;">0</span> INFO:   ***** Run HMMER on gene sequences *****</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="129" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

129

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<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC129" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff deletion" style="background-color: #fac5cd;">9</span>:5<span class="idiff deletion" style="background-color: #fac5cd;">0</span> INFO: Running 2093 job(s) on hmmsearch, starting at <span class="idiff deletion" style="background-color: #fac5cd;">12/05/2022</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff deletion" style="background-color: #fac5cd;">9</span>:5<span class="idiff right deletion" style="background-color: #fac5cd;">0</span></span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="130" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

130

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC130" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:39:54</span> INFO:        [hmmsearch]     210 of 2093 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

131

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC131" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">9:5</span>5 INFO:  [hmmsearch]     419 of 2093 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="132" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

132

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<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC132" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">9:5</span>6 INFO:  [hmmsearch]     628 of 2093 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="133" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

133

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<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC133" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">9:57</span> INFO:  [hmmsearch]     838 of 2093 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="134" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

134

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<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC134" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:39:58</span> INFO:        [hmmsearch]     1047 of 2093 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="135" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

135

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<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC135" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05</span> 1<span class="idiff deletion" style="background-color: #fac5cd;">6</span>:3<span class="idiff right deletion" style="background-color: #fac5cd;">9:59</span> INFO:  [hmmsearch]     1256 of 2093 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="136" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

136

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC136" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:40:0</span>1 INFO:        [hmmsearch]     1466 of 2093 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="137" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

137

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC137" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:40:0</span>2 INFO:        [hmmsearch]     1675 of 2093 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="138" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

138

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC138" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:40:02</span> INFO:        [hmmsearch]     1884 of 2093 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="139" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

139

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC139" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:40:0</span>4 INFO:        [hmmsearch]     2093 of 2093 task(s) completed</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="140" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

140

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC140" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:40:0</span>6 INFO:        Validating exons and removing overlapping matches</span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="141" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

141

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC141" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:40:0</span>8 INFO:        3 candidate overlapping regions found</span>

</pre></td>

</tr>

<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="142" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

142

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC142" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:40:0</span>8 INFO:        49 exons in total</span>

</pre></td>

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<tr class="line_holder old" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="143" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

143

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC143" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:40:1</span>0 INFO:        Results:        C:2.1%[S:2.1%,D:0.0%],F:0.0%,M:97.9%,n:2137        </span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

100

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC100" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:56</span> INFO:  Extract markers...</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

101

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC101" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:56</span> INFO:  Place the markers on the reference tree...</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

102

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC102" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff addition" style="background-color: #c7f0d2;">0:56</span> INFO:        Running 1 job(s) on sepp, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28</span>/202<span class="idiff addition" style="background-color: #c7f0d2;">3</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">0:56</span></span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

103

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC103" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">5:03</span> INFO:  [sepp]  1 of 1 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

104

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC104" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">5:03</span> INFO:  Lineage saccharomycetes is selected, supported by 18 markers out of 19</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="105" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

105

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC105" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">5:04</span> INFO:  Running BUSCO using lineage dataset saccharomycetes_odb10 (eukaryota, 2020-08-05)</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

106

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC106" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff addition" style="background-color: #c7f0d2;">5:04</span> INFO:        Running 1 job(s) on bbtools, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28</span>/202<span class="idiff addition" style="background-color: #c7f0d2;">3</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">5:04</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

107

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC107" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">5:06</span> INFO:  [bbtools]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="108" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

108

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC108" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff addition" style="background-color: #c7f0d2;">5:06</span> INFO:        Running 1 job(s) on metaeuk, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28</span>/202<span class="idiff addition" style="background-color: #c7f0d2;">3</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">5:06</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

109

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC109" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">5:13</span> INFO:  [metaeuk]       1 of 1 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="110" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

110

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC110" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">5:15</span> INFO:  ***** Run HMMER on gene sequences *****</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

111

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC111" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff addition" style="background-color: #c7f0d2;">5:15</span> INFO:        Running 2137 job(s) on hmmsearch, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28</span>/202<span class="idiff addition" style="background-color: #c7f0d2;">3</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">5:15</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="112" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

112

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC112" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff addition" style="background-color: #c7f0d2;">5</span>:1<span class="idiff right addition" style="background-color: #c7f0d2;">8</span> INFO:   [hmmsearch]     214 of 2137 task(s) completed</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

113

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC113" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">5:20</span> INFO:  [hmmsearch]     428 of 2137 task(s) completed</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

114

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC114" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">5:22</span> INFO:  [hmmsearch]     642 of 2137 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

115

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC115" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">5:24</span> INFO:  [hmmsearch]     855 of 2137 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="116" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

116

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC116" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff addition" style="background-color: #c7f0d2;">5</span>:2<span class="idiff right addition" style="background-color: #c7f0d2;">6</span> INFO:   [hmmsearch]     1069 of 2137 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="117" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

117

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC117" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff addition" style="background-color: #c7f0d2;">5</span>:2<span class="idiff right addition" style="background-color: #c7f0d2;">8</span> INFO:   [hmmsearch]     1283 of 2137 task(s) completed</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

118

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC118" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">5:30</span> INFO:  [hmmsearch]     1496 of 2137 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

119

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC119" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">5:32</span> INFO:  [hmmsearch]     1710 of 2137 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

120

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC120" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">5:34</span> INFO:  [hmmsearch]     1924 of 2137 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

121

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC121" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff addition" style="background-color: #c7f0d2;">5</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">8</span> INFO:   [hmmsearch]     2137 of 2137 task(s) completed</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

122

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC122" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">5:43</span> INFO:  Validating exons and removing overlapping matches</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

123

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC123" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">5:45</span> INFO:  0 candidate overlapping regions found</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="124" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

124

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC124" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">5:45</span> INFO:  45 exons in total</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

125

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC125" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">5:45</span> INFO:  Extracting missing and fragmented buscos from the file refseq_db.faa...</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

126

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC126" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff addition" style="background-color: #c7f0d2;">5:50</span> INFO:        Running 1 job(s) on metaeuk, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28</span>/202<span class="idiff addition" style="background-color: #c7f0d2;">3</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">5:50</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

127

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC127" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">5:57</span> INFO:  [metaeuk]       1 of 1 task(s) completed</span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

128

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC128" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff addition" style="background-color: #c7f0d2;">5</span>:5<span class="idiff right addition" style="background-color: #c7f0d2;">9</span> INFO:   ***** Run HMMER on gene sequences *****</span>

</pre></td>

</tr>

<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="129" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

129

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC129" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff addition" style="background-color: #c7f0d2;">5</span>:5<span class="idiff addition" style="background-color: #c7f0d2;">9</span> INFO: Running 2093 job(s) on hmmsearch, starting at <span class="idiff addition" style="background-color: #c7f0d2;">04/28/2023</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff addition" style="background-color: #c7f0d2;">5</span>:5<span class="idiff right addition" style="background-color: #c7f0d2;">9</span></span>

</pre></td>

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<tr class="line_holder new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

130

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC130" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:36:03</span> INFO:        [hmmsearch]     210 of 2093 task(s) completed</span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

131

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC131" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">6:0</span>5 INFO:  [hmmsearch]     419 of 2093 task(s) completed</span>

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<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

132

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC132" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">6:0</span>6 INFO:  [hmmsearch]     628 of 2093 task(s) completed</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="133" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

133

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC133" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">6:08</span> INFO:  [hmmsearch]     838 of 2093 task(s) completed</span>

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<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="134" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

134

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC134" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:36:09</span> INFO:        [hmmsearch]     1047 of 2093 task(s) completed</span>

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<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="135" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

135

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC135" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28</span> 1<span class="idiff addition" style="background-color: #c7f0d2;">4</span>:3<span class="idiff right addition" style="background-color: #c7f0d2;">6:10</span> INFO:  [hmmsearch]     1256 of 2093 task(s) completed</span>

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<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

136

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC136" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:36:1</span>1 INFO:        [hmmsearch]     1466 of 2093 task(s) completed</span>

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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

137

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC137" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:36:1</span>2 INFO:        [hmmsearch]     1675 of 2093 task(s) completed</span>

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<td class="new_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

138

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC138" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:36:13</span> INFO:        [hmmsearch]     1884 of 2093 task(s) completed</span>

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<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

139

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC139" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:36:1</span>4 INFO:        [hmmsearch]     2093 of 2093 task(s) completed</span>

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<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="140" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

140

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC140" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:36:1</span>6 INFO:        Validating exons and removing overlapping matches</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="141" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

141

</td>

<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC141" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:36:1</span>8 INFO:        3 candidate overlapping regions found</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="142" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

142

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC142" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:36:1</span>8 INFO:        49 exons in total</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

143

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC143" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:36:2</span>0 INFO:        Results:        C:2.1%[S:2.1%,D:0.0%],F:0.0%,M:97.9%,n:2137        </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

144

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<td class="new_line diff-line-num" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

144

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC144" class="line" lang="plaintext"></span>

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<td class="old_line diff-line-num old" data-linenumber="145" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

145

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC145" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:40:1</span>0 INFO:        </span>

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<td class="old_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

145

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC145" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:36:2</span>0 INFO:        </span>

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<td class="old_line diff-line-num" data-linenumber="146" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

146

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<td class="new_line diff-line-num" data-linenumber="146" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC146" class="line" lang="plaintext"></span>

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<td class="old_line diff-line-num" data-linenumber="147" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

147

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<td class="new_line diff-line-num" data-linenumber="147" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC147" class="line" lang="plaintext">   --------------------------------------------------</span>

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<td class="old_line diff-line-num" data-linenumber="148" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="148" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC148" class="line" lang="plaintext">   |Results from generic domain eukaryota_odb10      |</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="167" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="167" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -167,13 +167,13 @@</td>

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<td class="old_line diff-line-num" data-linenumber="167" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

167

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<td class="new_line diff-line-num" data-linenumber="167" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC167" class="line" lang="plaintext">   |2091   Missing BUSCOs (M)                        |</span>

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<td class="old_line diff-line-num" data-linenumber="168" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="168" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC168" class="line" lang="plaintext">   |2137   Total BUSCO groups searched               |</span>

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<td class="old_line diff-line-num" data-linenumber="169" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

169

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<td class="new_line diff-line-num" data-linenumber="169" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC169" class="line" lang="plaintext">   --------------------------------------------------</span>

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<td class="old_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

170

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<td class="new_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC170" class="line" lang="plaintext">202<span class="idiff left deletion" style="background-color: #fac5cd;">2-12-05 16:40:1</span>0 INFO:      BUSCO analysis done with WARNING(s). Total running time: <span class="idiff right deletion" style="background-color: #fac5cd;">373</span> seconds</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC170" class="line" lang="plaintext">202<span class="idiff left addition" style="background-color: #c7f0d2;">3-04-28 14:36:2</span>0 INFO:      BUSCO analysis done with WARNING(s). Total running time: <span class="idiff right addition" style="background-color: #c7f0d2;">449</span> seconds</span>

</pre></td>

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171

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<td class="new_line diff-line-num" data-linenumber="171" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC171" class="line" lang="plaintext"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="172" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

172

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<td class="new_line diff-line-num" data-linenumber="172" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

172

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC172" class="line" lang="plaintext">***** Summary of warnings: *****</span>

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<td class="old_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

173

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<td class="new_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC173" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:33:55</span> WARNING:busco.BuscoConfig    Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line.</span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="174" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

174

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<td class="new_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC174" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:34</span>:05 WARNING:busco.busco_tools.hmmer      BUSCO did not find any match. Make sure to check the log files if this is unexpected.</span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="175" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="173" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

173

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC173" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:28:49</span> WARNING:busco.BuscoConfig    Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line.</span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC174" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:29</span>:05 WARNING:busco.busco_tools.hmmer      BUSCO did not find any match. Make sure to check the log files if this is unexpected.</span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC175" class="line" lang="plaintext"></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC176" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:40:1</span>0 INFO:        Results written in /busco_wd/test_eukaryota</span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC177" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:40:1</span>0 INFO:        For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html</span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC176" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:36:2</span>0 INFO:        Results written in /busco_wd/test_eukaryota</span>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC177" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:36:2</span>0 INFO:        For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html</span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC179" class="line" lang="plaintext">202<span class="idiff left right deletion" style="background-color: #fac5cd;">2-12-05 16:40:1</span>0 INFO:        Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO</span></pre></td>

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC179" class="line" lang="plaintext">202<span class="idiff left right addition" style="background-color: #c7f0d2;">3-04-28 14:36:2</span>0 INFO:        Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO</span></pre></td>

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<br>

</li>

<li id="ecaba573b4d50cb889221b97937db25cede5aabb">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#ecaba573b4d50cb889221b97937db25cede5aabb"><strong style="font-weight: bold;">tests/unittests/AutoLineage_unittests.py</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="273" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -273,26 +273,24 @@ class TestAutoLineage(unittest.TestCase):</td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC273" class="line" lang="python">        <span class="n" style="color: #333;">mock_config3</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Mock</span><span class="p">()</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC274" class="line" lang="python">        <span class="n" style="color: #333;">mock_config1</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">.</span><span class="n" style="color: #333;">side_effect</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC275" class="line" lang="python">            <span class="s" style="color: #d14;">"test_input1"</span><span class="p">,</span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC276" class="line" lang="python">            <span class="s" style="color: #d14;">"prok_tran"</span><span class="p">,</span></span>

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC277" class="line" lang="python">            <span class="s" style="color: #d14;">"prokaryota"</span><span class="p">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="276" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC276" class="line" lang="python">            <span class="s" style="color: #d14;">"test_lineage1"</span><span class="p">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="279" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="277" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC277" class="line" lang="python">            <span class="s" style="color: #d14;">"test_lineage1"</span><span class="p">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="280" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="278" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC278" class="line" lang="python">        <span class="p">]</span></span>

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<td class="old_line diff-line-num" data-linenumber="281" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="279" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC279" class="line" lang="python">        <span class="n" style="color: #333;">mock_config2</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">.</span><span class="n" style="color: #333;">side_effect</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

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<td class="old_line diff-line-num" data-linenumber="282" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="280" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC280" class="line" lang="python">            <span class="s" style="color: #d14;">"test_input2"</span><span class="p">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="283" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="281" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC283" class="line" lang="python">            <span class="s" style="color: #d14;">"prok_tran"</span><span class="p">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="284" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="281" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC284" class="line" lang="python">            <span class="s" style="color: #d14;">"prokaryota"</span><span class="p">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="285" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="281" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC281" class="line" lang="python">            <span class="s" style="color: #d14;">"test_lineage2"</span><span class="p">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="286" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="282" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC282" class="line" lang="python">            <span class="s" style="color: #d14;">"test_lineage2"</span><span class="p">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="287" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="283" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC283" class="line" lang="python">        <span class="p">]</span></span>

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<td class="old_line diff-line-num" data-linenumber="288" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="284" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC284" class="line" lang="python">        <span class="n" style="color: #333;">mock_config3</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">.</span><span class="n" style="color: #333;">side_effect</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

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<td class="old_line diff-line-num" data-linenumber="289" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="285" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC285" class="line" lang="python">            <span class="s" style="color: #d14;">"test_input3"</span><span class="p">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="290" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

290

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<td class="new_line diff-line-num old" data-linenumber="286" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC290" class="line" lang="python">            <span class="s" style="color: #d14;">"euk_tran"</span><span class="p">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="291" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="286" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC291" class="line" lang="python">            <span class="s" style="color: #d14;">"eukaryota"</span><span class="p">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="292" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="286" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC286" class="line" lang="python">            <span class="s" style="color: #d14;">"test_lineage3"</span><span class="p">,</span></span>

</pre></td>

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC287" class="line" lang="python">            <span class="s" style="color: #d14;">"test_lineage3"</span><span class="p">,</span></span>

</pre></td>

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294

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<td class="new_line diff-line-num" data-linenumber="288" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC288" class="line" lang="python">        <span class="p">]</span></span>

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<td class="old_line diff-line-num" data-linenumber="295" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="289" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC289" class="line" lang="python"></span>

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<td class="old_line diff-line-num new" data-linenumber="296" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="290" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

290

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC290" class="line" lang="python">        <span class="n" style="color: #333;">mock_config1</span><span class="p">.</span><span class="n" style="color: #333;">update_mode</span><span class="p">.</span><span class="n" style="color: #333;">side_effect</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="s" style="color: #d14;">"prok_tran"</span><span class="p">,</span> <span class="s" style="color: #d14;">"prokaryota"</span><span class="p">)]</span></span>

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<td class="old_line diff-line-num new" data-linenumber="296" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="291" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

291

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC291" class="line" lang="python">        <span class="n" style="color: #333;">mock_config2</span><span class="p">.</span><span class="n" style="color: #333;">update_mode</span><span class="p">.</span><span class="n" style="color: #333;">side_effect</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="s" style="color: #d14;">"prok_tran"</span><span class="p">,</span> <span class="s" style="color: #d14;">"prokaryota"</span><span class="p">)]</span></span>

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<td class="old_line diff-line-num new" data-linenumber="296" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="292" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

292

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC292" class="line" lang="python">        <span class="n" style="color: #333;">mock_config3</span><span class="p">.</span><span class="n" style="color: #333;">update_mode</span><span class="p">.</span><span class="n" style="color: #333;">side_effect</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="s" style="color: #d14;">"prok_tran"</span><span class="p">,</span> <span class="s" style="color: #d14;">"eukaryota"</span><span class="p">)]</span></span>

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<td class="old_line diff-line-num new" data-linenumber="296" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="293" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

293

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC293" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="296" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

296

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<td class="new_line diff-line-num" data-linenumber="294" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC294" class="line" lang="python">        <span class="n" style="color: #333;">mock_analysis1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Mock</span><span class="p">()</span></span>

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<td class="old_line diff-line-num" data-linenumber="297" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="295" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC295" class="line" lang="python">        <span class="n" style="color: #333;">mock_analysis2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Mock</span><span class="p">()</span></span>

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<td class="old_line diff-line-num" data-linenumber="298" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="296" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC296" class="line" lang="python">        <span class="n" style="color: #333;">mock_analysis3</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Mock</span><span class="p">()</span></span>

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<br>

</li>

<li id="480430e97df92c2ae922e852fe89a5f357c98cda">

<a href="https://salsa.debian.org/med-team/busco/-/commit/d23c473b384dae3ebfe65de449a0fba5ab0367ee#480430e97df92c2ae922e852fe89a5f357c98cda"><strong style="font-weight: bold;">tests/unittests/GenomeAnalysis_unittests.py</strong></a>

<hr style="overflow: hidden; border: 1px solid #e1e1e1;">

<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -7,8 +7,6 @@ class TestConfigManager(unittest.TestCase):</td>

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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

8

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

8

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="python">        <span class="k" style="font-weight: 600;">pass</span></span>

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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

9

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

9

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC9" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

10

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<td class="new_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># @patch('busco.analysis.GenomeAnalysis.BuscoAnalysis.config.get', return_value="test")</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

11

</td>

<td class="new_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC11" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># @patch('busco.analysis.GenomeAnalysis.BuscoAnalysis.config.getboolean', return_value=True)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

12

</td>

<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

10

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10" class="line" lang="python">    <span class="nd">@patch</span><span class="p">(</span><span class="s" style="color: #d14;">"busco.analysis.GenomeAnalysis.BuscoAnalysis.config"</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

13

</td>

<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

11

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC11" class="line" lang="python">    <span class="nd">@patch</span><span class="p">(</span><span class="s" style="color: #d14;">"busco.analysis.BuscoAnalysis.os.path"</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

14

</td>

<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

12

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC12" class="line" lang="python">    <span class="nd">@patch</span><span class="p">(</span><span class="s" style="color: #d14;">"busco.analysis.GenomeAnalysis.NucleotideAnalysis.check_nucleotide_file"</span><span class="p">)</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -21,7 +19,6 @@ class TestConfigManager(unittest.TestCase):</td>

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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

21

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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

19

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC19" class="line" lang="python">        <span class="s" style="color: #d14;">"busco.analysis.GenomeAnalysis.BuscoAnalysis.config.get"</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

22

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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

20

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC20" class="line" lang="python">        <span class="n" style="color: #333;">return_value</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"euk_genome_aug"</span><span class="p">,</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

23

</td>

<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

21

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC21" class="line" lang="python">    <span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

24

</td>

<td class="new_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC24" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># @patch('busco.analysis.GenomeAnalysis.BuscoAnalysis.config.getboolean')</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

25

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<td class="new_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

22

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC22" class="line" lang="python">    <span class="nd">@patch</span><span class="p">(</span><span class="s" style="color: #d14;">"busco.analysis.GenomeAnalysis.BuscoAnalysis.config"</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

26

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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

23

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC23" class="line" lang="python">    <span class="nd">@patch</span><span class="p">(</span><span class="s" style="color: #d14;">"busco.analysis.Analysis.logger.warning"</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

27

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<td class="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

24

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC24" class="line" lang="python">    <span class="nd">@patch</span><span class="p">(</span><span class="s" style="color: #d14;">"busco.analysis.GenomeAnalysis.BBToolsRunner"</span><span class="p">)</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -47,6 +44,7 @@ class TestConfigManager(unittest.TestCase):</td>

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<td class="old_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC44" class="line" lang="python">        <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

45

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC45" class="line" lang="python">    <span class="p">):</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

49

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<td class="new_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC46" class="line" lang="python">        <span class="n" style="color: #333;">analysis</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GenomeAnalysis</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">GenomeAnalysisEukaryotesAugustus</span><span class="p">()</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC47" class="line" lang="python">        <span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">domain</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"eukaryota"</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

50

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<td class="new_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC48" class="line" lang="python">        <span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">init_tools</span><span class="p">()</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="51" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

51

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<td class="new_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC49" class="line" lang="python">        <span class="n" style="color: #333;">mock_hmmer</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">assert_called</span><span class="p">()</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

52

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<td class="new_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC50" class="line" lang="python">        <span class="n" style="color: #333;">mock_mkblast</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">assert_called</span><span class="p">()</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="71" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -71,6 +69,7 @@ class TestConfigManager(unittest.TestCase):</td>

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<td class="new_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC69" class="line" lang="python">        <span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">mock_hmmer</span><span class="p">,</span> <span class="n" style="color: #333;">mock_metaeuk</span><span class="p">,</span> <span class="n" style="color: #333;">mock_bbtools</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span></span>

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<td class="old_line diff-line-num" data-linenumber="72" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC70" class="line" lang="python">    <span class="p">):</span></span>

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<td class="old_line diff-line-num" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="71" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC71" class="line" lang="python">        <span class="n" style="color: #333;">analysis</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GenomeAnalysis</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">GenomeAnalysisEukaryotesMetaeuk</span><span class="p">()</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC72" class="line" lang="python">        <span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">domain</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"eukaryota"</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="74" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC73" class="line" lang="python">        <span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">init_tools</span><span class="p">()</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="74" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC74" class="line" lang="python">        <span class="n" style="color: #333;">mock_hmmer</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">assert_called</span><span class="p">()</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC75" class="line" lang="python">        <span class="n" style="color: #333;">mock_metaeuk</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">assert_called</span><span class="p">()</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="89" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="88" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -89,6 +88,7 @@ class TestConfigManager(unittest.TestCase):</td>

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<td class="new_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC88" class="line" lang="python">        <span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">mock_hmmer</span><span class="p">,</span> <span class="n" style="color: #333;">mock_prodigal</span><span class="p">,</span> <span class="n" style="color: #333;">mock_bbtools</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span></span>

</pre></td>

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<td class="new_line diff-line-num" data-linenumber="89" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC89" class="line" lang="python">    <span class="p">):</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="91" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

91

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<td class="new_line diff-line-num" data-linenumber="90" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

90

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC90" class="line" lang="python">        <span class="n" style="color: #333;">analysis</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GenomeAnalysis</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">GenomeAnalysisProkaryotes</span><span class="p">()</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">

91

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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC91" class="line" lang="python">        <span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">domain</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"prokaryota"</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

92

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<td class="new_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

92

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC92" class="line" lang="python">        <span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">init_tools</span><span class="p">()</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

93

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<td class="new_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC93" class="line" lang="python">        <span class="n" style="color: #333;">mock_hmmer</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">assert_called</span><span class="p">()</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

94

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<td class="new_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

94

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC94" class="line" lang="python">        <span class="n" style="color: #333;">mock_prodigal</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">assert_called</span><span class="p">()</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="122" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="122" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>

<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -122,16 +122,5 @@ class TestConfigManager(unittest.TestCase):</td>

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<td class="new_line diff-line-num" data-linenumber="122" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC122" class="line" lang="python">        <span class="n" style="color: #333;">mock_run_bbtools</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">assert_called</span><span class="p">()</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="123" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="new_line diff-line-num" data-linenumber="123" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC123" class="line" lang="python">        <span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">write_gff_files</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">assert_called</span><span class="p">()</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

124

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<td class="new_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC124" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

125

</td>

<td class="new_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC125" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># @patch('busco.GenomeAnalysis.GenomeAnalysisEukaryotesAugustus._rerun_analysis')</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

126

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<td class="new_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC126" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># @patch('busco.GenomeAnalysis.GenomeAnalysisEukaryotesAugustus.run_hmmer')</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="127" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

127

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<td class="new_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC127" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># @patch('busco.GenomeAnalysis.GenomeAnalysisEukaryotesAugustus._run_augustus')</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="128" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

128

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<td class="new_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC128" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># @patch('busco.GenomeAnalysis.BLASTAnalysis._run_tblastn')</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="129" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

129

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<td class="new_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC129" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># @patch('busco.GenomeAnalysis.BLASTAnalysis._run_mkblast')</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="130" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

130

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<td class="new_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC130" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># mock_mkblast.assert_called()</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

131

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<td class="new_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC131" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># mock_tblastn.assert_called()</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="132" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

132

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<td class="new_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC132" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># mock_augustus.assert_called()</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="133" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

133

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<td class="new_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC133" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># mock_hmmer.assert_called()</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="134" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

134

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<td class="new_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC134" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># mock_rerun.assert_called()</span></span>

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<td class="old_line diff-line-num old" data-linenumber="135" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

135

</td>

<td class="new_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC135" class="line" lang="python"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="136" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

136

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<td class="new_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

125

</td>

<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC125" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tearDown</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="137" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

137

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<td class="new_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">

126

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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC126" class="line" lang="python">        <span class="k" style="font-weight: 600;">pass</span></span></pre></td>

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