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GitLab

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<h3>

Andreas Tille pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/proteinortho">Debian Med / proteinortho</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/50d748b5c10ee4ec1db1c0ec09e45d0f0dddb9cf">50d748b5</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2022-01-24T18:17:27+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 6.0.33+dfsg</pre>

</li>

</ul>

<h4>9 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">

.gitignore

</a>

</li>

<li class="file-stats">

<a href="#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">

CHANGELOG

</a>

</li>

<li class="file-stats">

<a href="#ff6936350384213d6f693f4d604134188ce088c8">

CHANGEUID

</a>

</li>

<li class="file-stats">

<a href="#c9e37a96ac72f9ef076d7a41a57470524d63b36e">

proteinortho6.pl

</a>

</li>

<li class="file-stats">

<a href="#e88e2072d8bed1edd8ac79e979262281cfe9549b">

src/.gitlab-ci.yml

</a>

</li>

<li class="file-stats">

<a href="#3439148ea7017354388f7c55043cc84986c1c394">

src/proteinortho_grab_proteins.pl

</a>

</li>

<li class="file-stats">

<a href="#b449ded4202264f363300e737ee12e8592179216">

test/C.faa

</a>

</li>

<li class="file-stats">

<a href="#775bfcb5ef827787daeffc1708e26d3be7407847">

test/C.gff

</a>

</li>

<li class="file-stats">

<a href="#314f9d77838daf9ce75df9af4e3e5cbae36dbaf9">

test/C2.faa

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="a5cc2925ca8258af241be7e5b0381edf30266302">

<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/50d748b5c10ee4ec1db1c0ec09e45d0f0dddb9cf#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,6 +9,7 @@ test/*.psq</td>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">test.*</span>

</pre>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">.log</span>

</pre>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">*cache*</span>

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12

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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">dev/*</span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">backup/*</span>

</pre>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>

</pre>

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<br>

</li>

<li id="1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">

<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/50d748b5c10ee4ec1db1c0ec09e45d0f0dddb9cf#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a"><strong>CHANGELOG</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -83,31 +83,31 @@</td>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext">             added support for tblastx+ and tblastx legacy </span>

</pre>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext">             thanks to Clemens Thölken</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext">2018    ** Proteinortho6 **</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext">     20. Jun<span class="idiff left">i</span>-4.Jul<span class="idiff right">i</span></span>

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<td class="old_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">     20. Jun<span class="idiff left">e</span>-4.Jul<span class="idiff right">y</span></span>

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<td class="old_line diff-line-num" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext">             openmp support (max_of_diag,get_new_x,makeOrthogonal,normalize,getY)</span>

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<td class="old_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext">             bitscore integration in the convergence (weighted algebraic connectivity)</span>

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<td class="old_line diff-line-num" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext">             protein output is now sorted in descending degree-order (sort with comparator_pairDoubleUInt)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext">             getConnectivity: special case checks now if the induced subgraph is complete (K_n)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext">             added various test functions</span>

</pre>

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92

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext">     5. Jul<span class="idiff left right">i</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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92

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">     5. Jul<span class="idiff left right">y</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

93

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext">             added kmere heuristic for splitting groups in proteinortho_clustering. After the calculation of an fiedler vector, the kmere heuristic splits the graph not only in the positive and negative entries of the vector but in k clusters. k=2 -> the original split (without the purity).  </span>

</pre>

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94

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext">     16. Jul<span class="idiff left right">i</span></span>

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<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">     16. Jul<span class="idiff left right">y</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

95

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext">             added LAPACK support for CC with less than 2^15 nodes (since it uses quadratic space -> (2^15)^2=2^30) for the calculation of the algebraic connectivity.</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

96

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96

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext">             added all other proteinortho files to this repository.</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

97

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext">             graphMinusRemoveGraph.cpp implements proteinortho5_clean_edges2.pl in c++</span>

</pre>

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98

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="plaintext">     23.Jul<span class="idiff left right">i</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">     23.Jul<span class="idiff left right">y</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

99

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<td class="new_line diff-line-num" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext">             openMP support for laplacian declaration (for lapack).</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

100

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<td class="new_line diff-line-num" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

100

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext">            'make test' clean up.</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

101

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<td class="new_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

101

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext">            jackhmmer, phmmer, diamond, usearch support.</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="plaintext">    24 Jul<span class="idiff left right">i</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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102

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">    24 Jul<span class="idiff left right">y</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

103

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<td class="new_line diff-line-num" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

103

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext">            last integration.</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

104

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<td class="new_line diff-line-num" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

104

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext">            phmmer+jackhmmer fix/workaround (there is no local identity in the output -> disabled).</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

105

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<td class="new_line diff-line-num" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

105

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext">            proteinortho.pl : set cluster algorithm to weighted-mode as default.</span>

</pre>

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106

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<td class="new_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext">    30. Jul<span class="idiff left right">i</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">    30. Jul<span class="idiff left right">y</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext">            rapsearch integration.</span>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="plaintext">            proteinortho_clustering.cpp : -ramLapack is now -ram and is the threshold for laplace matrix + graph struct. </span>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext">            added dynamic memory management (proteinortho.pl + clustering.cpp) using the free -m command (if exists) </span>

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext">    31. Jul<span class="idiff left right">i</span></span>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">    31. Jul<span class="idiff left right">y</span></span>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="plaintext">            rapsearch fix (wrong order of db and q)</span>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="plaintext">            purity is back, now 0.1 (and fallback function, if all nodes are below purity threshold -> remove purity for this connected component)</span>

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="plaintext">            more options for proteinortho.pl -p=diamond-moresensitive|usearch-ublast</span>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="plaintext">            BUGfix in the DFS calculation (recursion in c++ failed with segmentation fault if the recursion was too deep) -> now iteratively (memory ineffciently) with Queue</span>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="plaintext">    10. Okt</span>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="plaintext">            DFS -> BFS since recursive calls can only be so deep.</span>

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<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext">    18. <span class="idiff left right"> </span>Okt</span>

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">    18. Okt</span>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="plaintext">            purity is now 1e-7, evalue 1e-8 (http://people.sc.fsu.edu/~jburkardt/c_src/power_method/power_method_prb.c)</span>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="plaintext">            kmere heuristic minNodes = 2^20 (~1e+6), kmere now checks if the "normal" split would result in a good partition.</span>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="plaintext">    30. Okt</span>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="plaintext">            -selfblast generates duplicated hits -> automatically calls cleanupblastgraph</span>

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="plaintext">    3. Juni (uid:3142)</span>

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="plaintext">            refined error messages on duplicated inputs, <2 inputs</span>

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<pre style="margin: 0;">-<span id="LC209" class="line" lang="plaintext">    27. Jun<span class="idiff left right">i</span> (uid:3492)</span>

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">    27. Jun<span class="idiff left right">e</span> (uid:3492)</span>

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="plaintext">            proteinortho6.pl now writes databases (-step=1) into -tmp directory if system call failed.</span>

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="plaintext">            fixed small issue that tmp directories are created inside eachother. </span>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="plaintext">            better stderr outputs e.g. if blast fails -> try -check ...</span>

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<pre style="margin: 0;">-<span id="LC213" class="line" lang="plaintext">    1. Jul<span class="idiff left right">i</span> (uid:3511)</span>

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">    1. Jul<span class="idiff left right">y</span> (uid:3511)</span>

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="plaintext">            fixed the -ram issue (used free memory, now total memory) in case there is a swap using up all free memory (also proteinortho_clustering now throws a warning not a error)</span>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="plaintext">    10. Juli (uid:3697)</span>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="plaintext">            fixed proteinortho_grab_proteins.pl: -tofiles option now escapes if -exact, replaced chomp with s/[\r\n]+$//</span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -250,13 +250,13 @@</td>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="plaintext">    29. April (4799)</span>

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="plaintext">            improved error messages (e.g. for missmatching files with --synteny)</span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="plaintext">            fixed small bugs for --synteny and the *.summary, *.html files</span>

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<td class="new_line diff-line-num old" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC253" class="line" lang="plaintext">    12. Jun<span class="idiff left right">i</span> (4999)</span>

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext">    12. Jun<span class="idiff left right">e</span> (4999)</span>

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="plaintext">            reduced the IO work by directly importing the diamond results to proteinortho (no temporary file is generated, except if -keep is set). </span>

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="plaintext">            same ^ for ncbi-blast+ </span>

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<td class="old_line diff-line-num" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="plaintext">            added -mtune -march g++ compiler options for the clustering script</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC257" class="line" lang="plaintext">    18. Jun<span class="idiff left right">i</span> (5000)</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext">    18. Jun<span class="idiff left right">e</span> (5000)</span>

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="plaintext">            the -mtune and -march options are now optional due to some incompatibility...</span>

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<pre style="margin: 0;">-<span id="LC259" class="line" lang="plaintext">    14. Jul<span class="idiff left right">i</span> (5029)</span>

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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext">    14. Jul<span class="idiff left right">y</span> (5029)</span>

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="plaintext">            fixed a small bug, s.t. if write permission is missing in the directory of the fasta files, then the database files are generated in the tmp directory properly.</span>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="plaintext">    4. Aug (5090)</span>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="plaintext">            proteinortho_clustering now properly displays progress (Clusterin: 10%, 20% ...)</span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -297,5 +297,13 @@</td>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="plaintext">    6. April (5584)</span>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="plaintext">            fixed a bug, where generated databases are always overwritten (https://gitlab.com/paulklemm_PHD/proteinortho/-/issues/48). Thanks to Bjoern </span>

</pre>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="plaintext">            fixed another bug that caused the compilation of proteinortho_clustering to fail on CentOS (OMP_PROC_BIND=true) (https://gitlab.com/paulklemm_PHD/proteinortho/-/issues/39). </span>

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<pre style="margin: 0;">-<span id="LC300" class="line" lang="plaintext">    20. Juli (5594)</span>

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<pre style="margin: 0;">-<span id="LC301" class="line" lang="plaintext">            Makefile modification to account for issue 51+52: the -mtune and -march option are now totally optional.</span></pre>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext">    20. June (5594)</span>

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext">            Makefile modification to account for issue 51+52 (https://gitlab.com/paulklemm_PHD/proteinortho/-/issues): the -mtune and -march option are now totally optional, use 'make MTUNEARCH=TRUE all' to enable those features.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext">    7. July (5630)</span>

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<td class="new_line diff-line-num new" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext">            Improving error messages for step=1 and 2.</span>

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<td class="new_line diff-line-num new" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext">    23. Dec (5699)</span>

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<td class="new_line diff-line-num new" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext">            Fixed a bug for fasta headers with comma (generate a _clean version with ; instead of ,)</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext">    18. Jan (5733)</span>

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<td class="new_line diff-line-num new" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext">            Fixed a bug if a faa sequence only contains fna symbols (#55), now diamond will automatically restart with the --ignore-warnings option. </span>

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<td class="new_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext">            Added a new option to add parameters to the database generation step 2 (--subparaMakeBlast), thanks to @kullrich</span>

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext">            Fixed 2 small bugs (a) binaries could not be found in $PATH (changed whereis to which) and (b) the database generation never fails (now it does...)</span></pre>

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</li>

<li id="ff6936350384213d6f693f4d604134188ce088c8">

<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/50d748b5c10ee4ec1db1c0ec09e45d0f0dddb9cf#ff6936350384213d6f693f4d604134188ce088c8"><strong>CHANGEUID</strong></a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">5<span class="idiff left right">594</span></span></pre>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">5<span class="idiff left right">733</span></span></pre>

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<li id="c9e37a96ac72f9ef076d7a41a57470524d63b36e">

<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/50d748b5c10ee4ec1db1c0ec09e45d0f0dddb9cf#c9e37a96ac72f9ef076d7a41a57470524d63b36e"><strong>proteinortho6.pl</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -183,6 +183,12 @@ additional parameters for the search tool (-p=blast,diamond,...) example -subpar</td>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=back</span></span>

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="perl"></span>

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=item B<--subparaMakeBlast>='options'</span></span>

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="perl"></span>

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">additional parameters for the database generation (-p=blast -> makeblastdb,diamond -> diamond makedb,...) example -subpara='--ignore-warnings' for a common diamond error</span></span>

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="perl"></span>

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=back</span></span>

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=head2 Synteny options (optional, step 2)</span></span>

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC194" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">(output: <myproject>.ffadj-graph, <myproject>.poff-graph.tsv)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -473,7 +479,7 @@ use POSIX;</td>

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<pre style="margin: 0;"> <span id="LC479" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>

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<td class="new_line diff-line-num" data-linenumber="480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC480" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Variables</span></span>

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<pre style="margin: 0;"> <span id="LC481" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC476" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">6.0.3<span class="idiff left right">1</span></span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC482" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">6.0.3<span class="idiff left right">3</span></span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

477

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<td class="new_line diff-line-num" data-linenumber="483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC483" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span>    <span class="c1" style="color: #998; font-style: italic;"># 0/1/2/3 -> do all / only apply step 1 / only apply step 2 / only apply step 3</span></span>

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<td class="old_line diff-line-num" data-linenumber="478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

478

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<td class="new_line diff-line-num" data-linenumber="484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC484" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># 0/1   -> don't / be verbose</span></span>

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<td class="old_line diff-line-num" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC485" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$debug</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span>   <span class="c1" style="color: #998; font-style: italic;"># 0/1   -> don't / show debug data</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -503,6 +509,7 @@ our $twilight = 0;</td>

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<pre style="margin: 0;"> <span id="LC509" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$singles</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" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC510" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$clean</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC511" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$blastOptions</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="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC512" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$makeBlastOptions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

506

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<td class="new_line diff-line-num" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC513" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$clusterOptions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC514" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$nograph</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC515" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$doxml</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -645,6 +652,7 @@ foreach my $option (@ARGV) {</td>

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<td class="old_line diff-line-num" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC652" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?desc$/</span><span class="p">)</span>     <span class="p">{</span> <span class="nv" style="color: #008080;">$desc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC653" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?project=(.*)$/</span><span class="p">)</span>   <span class="p">{</span> <span class="nv" style="color: #008080;">$project</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="nv" style="color: #008080;">$project</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[\/* \t\:\~\&\%\$\§\"\(\)\[\]\{\}\^\\]//g</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC654" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?(subparaBlast|subpara)=(.*)$/i</span><span class="p">)</span>  <span class="p">{</span> <span class="nv" style="color: #008080;">$blastOptions</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">2</span><span class="p">;}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC655" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?(subparaMakeBlast)=(.*)$/i</span><span class="p">)</span>  <span class="p">{</span> <span class="nv" style="color: #008080;">$makeBlastOptions</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">2</span><span class="p">;}</span></span>

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<td class="old_line diff-line-num" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

648

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<td class="new_line diff-line-num" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

656

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<pre style="margin: 0;"> <span id="LC656" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?subparaCluster=(.*)$/i</span><span class="p">)</span>  <span class="p">{</span> <span class="nv" style="color: #008080;">$clusterOptions</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>

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<td class="old_line diff-line-num" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

649

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<td class="new_line diff-line-num" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

657

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<pre style="margin: 0;"> <span id="LC657" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?v(ersion)?$/i</span><span class="p">)</span>  <span class="p">{</span> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$version</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span> <span class="nb" style="color: #0086b3;">exit</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" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

650

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<td class="new_line diff-line-num" data-linenumber="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

658

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<pre style="margin: 0;"> <span id="LC658" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">!~</span> <span class="sr" style="color: #009926;">/^-/</span><span class="p">)</span>       <span class="p">{</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">exists</span><span class="p">(</span><span class="nv" style="color: #008080;">$files_map</span><span class="p">{</span><span class="nv" style="color: #008080;">$option</span><span class="p">})){</span><span class="nv" style="color: #008080;">$files_map</span><span class="p">{</span><span class="nv" style="color: #008080;">$option</span><span class="p">}</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: #008080;">@files</span><span class="p">,</span><span class="nv" style="color: #008080;">$option</span><span class="p">);}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> The input </span><span class="si" style="color: #d14;">$option</span><span class="s2" style="color: #d14;"> was is skipped, since it was allready given as input.</span><span class="si" style="color: #d14;">$NC</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Press 'strg+c' to prevent me from proceeding or wait 10 seconds to continue...</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nb" style="color: #0086b3;">sleep</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Well then, proceeding...</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span> <span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -748,7 +756,12 @@ sub reset_locale{</td>

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<td class="old_line diff-line-num" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

748

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<td class="new_line diff-line-num" data-linenumber="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

756

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<pre style="margin: 0;"> <span id="LC756" class="line" lang="perl"><span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

749

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<td class="new_line diff-line-num" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

757

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<pre style="margin: 0;"> <span id="LC757" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

750

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<td class="new_line diff-line-num" data-linenumber="758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

758

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<pre style="margin: 0;"> <span id="LC758" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">get_parameter</span><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

751

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<td class="new_line diff-line-num old" data-linenumber="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC751" class="line" lang="perl">  <span class="k" style="font-weight: 600;">return</span> <span class="p">"</span><span class="s2" style="color: #d14;">Parameter-vector : (</span><span class="p">",'</span><span class="s1" style="color: #d14;">version</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$version</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">step</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$step</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">verbose</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$verbose</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">debug</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$debug</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">exactstep3</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$exactstep3</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">synteny</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$synteny</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">duplication</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$duplication</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">cs</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$cs</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">alpha</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$alpha</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">connectivity</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$connectivity</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">cpus</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$cpus</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">evalue</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$evalue</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">purity</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$purity</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">coverage</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$coverage</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">identity</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$identity</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">blastmode</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$blastmode</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">sim</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$sim</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">report</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$report</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">keep</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$keep</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">force</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$force</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">selfblast</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$selfblast</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">twilight</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$twilight</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">singles</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$singles</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">clean</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$clean</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">blastOptions</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$blastOptions</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">nograph</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$nograph</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">xml</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$doxml</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">desc</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$desc</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">tmp_path</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">blastversion</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$blastversion</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">binpath</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$binpath</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">makedb</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$makedb</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">blast</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$blast</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">jobs_todo</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$jobs_todo</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">project</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$project</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">po_path</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$po_path</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">run_id</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$run_id</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">threads_per_process</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$threads_per_process</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">","</span><span class="s2" style="color: #d14;">useMcl</span><span class="p">","</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$useMcl</span><span class="p">",'</span><span class="s1" style="color: #d14;">,freemem</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$freemem_inMB</span><span class="p">","</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC759" class="line" lang="perl">  <span class="k" style="font-weight: 600;">return</span> <span class="p">"</span><span class="s2" style="color: #d14;">Parameter-vector : (</span><span class="p">",'</span><span class="s1" style="color: #d14;">version</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$version</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">step</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$step</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">verbose</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$verbose</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">debug</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$debug</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">exactstep3</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$exactstep3</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">synteny</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$synteny</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">duplication</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$duplication</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">cs</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$cs</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">alpha</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$alpha</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">connectivity</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$connectivity</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">cpus</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$cpus</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">evalue</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$evalue</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">purity</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$purity</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">coverage</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$coverage</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">identity</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$identity</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">blastmode</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$blastmode</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">sim</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$sim</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">report</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$report</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">keep</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$keep</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">force</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$force</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">selfblast</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$selfblast</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">twilight</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$twilight</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">singles</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$singles</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">clean</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$clean</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">blastOptions</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$blastOptions</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">makeBlastOptions</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$makeBlastOptions</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">nograph</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$nograph</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">xml</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$doxml</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">desc</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$desc</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">tmp_path</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">blastversion</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$blastversion</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">binpath</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$binpath</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">makedb</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$makedb</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">blast</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$blast</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">jobs_todo</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$jobs_todo</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">project</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$project</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">po_path</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$po_path</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">run_id</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$run_id</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">threads_per_process</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$threads_per_process</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">","</span><span class="s2" style="color: #d14;">useMcl</span><span class="p">","</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$useMcl</span><span class="p">",'</span><span class="s1" style="color: #d14;">,freemem</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$freemem_inMB</span><span class="p">","</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

760

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<pre style="margin: 0;">+<span id="LC760" class="line" lang="perl"><span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

761

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC761" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

762

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<pre style="margin: 0;">+<span id="LC762" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">uniq</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

763

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<pre style="margin: 0;">+<span id="LC763" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">%seen</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

764

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<pre style="margin: 0;">+<span id="LC764" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">grep</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$seen</span><span class="p">{</span><span class="vg" style="color: #008080;">$_</span><span class="p">}</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="nv" style="color: #008080;">@_</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

752

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<td class="new_line diff-line-num" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

765

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<pre style="margin: 0;"> <span id="LC765" class="line" lang="perl"><span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

753

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<td class="new_line diff-line-num" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

766

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<pre style="margin: 0;"> <span id="LC766" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

754

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<td class="new_line diff-line-num" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

767

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<pre style="margin: 0;"> <span id="LC767" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="p">"</span><span class="si" style="color: #d14;">$project</span><span class="s2" style="color: #d14;">.proteinortho.tsv</span><span class="p">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span> <span class="p">(</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">3</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$step</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="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -820,6 +833,16 @@ if($step < 3){ # don't check blast-bins (e.g. diamond) for step 3=clustering (no</td>

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<td class="old_line diff-line-num" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

820

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<td class="new_line diff-line-num" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

833

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<pre style="margin: 0;"> <span id="LC833" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

821

</td>

<td class="new_line diff-line-num" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

834

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<pre style="margin: 0;"> <span id="LC834" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$keep</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$cpus</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">8</span> <span class="p">){</span> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">!!!</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[Warning]:</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> The '-keep' option can result in a I/O bottleneck if used with many cores !!!</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$NC</span><span class="p">";</span> <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

822

</td>

<td class="new_line diff-line-num" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

835

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<pre style="margin: 0;"> <span id="LC835" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

836

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC836" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># 6.0.32 check if there are _clean files available -> use it instead. </span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

837

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC837" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">search_clean_file</span><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

838

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC838" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

839

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<pre style="margin: 0;">+<span id="LC839" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file_clean</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">abs_path</span> <span class="nv" style="color: #008080;">$file</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

840

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<pre style="margin: 0;">+<span id="LC840" class="line" lang="perl">  <span class="nv" style="color: #008080;">$file_clean</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/(\.[^.]+)$/_clean$1/</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

841

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<pre style="margin: 0;">+<span id="LC841" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$file_clean</span><span class="p">){</span><span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: #008080;">$file_clean</span><span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

842

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC842" class="line" lang="perl">  <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: #008080;">$file</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

843

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC843" class="line" lang="perl"><span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

844

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC844" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">4</span><span class="p">){</span> <span class="vg" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">search_clean_file</span><span class="p">(</span><span class="vg" style="color: #008080;">$_</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="nv" style="color: #008080;">@files</span><span class="p">;</span> <span class="nv" style="color: #008080;">@files</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">uniq</span> <span class="nv" style="color: #008080;">@files</span> <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

845

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC845" class="line" lang="perl"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

823

</td>

<td class="new_line diff-line-num" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

846

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC846" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># do uniprot _additional* file appending for --isoform</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

824

</td>

<td class="new_line diff-line-num" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

847

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<pre style="margin: 0;"> <span id="LC847" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$isoform</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">uniprot</span><span class="p">"){</span> </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

825

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<td class="new_line diff-line-num" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

848

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<pre style="margin: 0;"> <span id="LC848" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">preparing files for isoform processing.</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -858,6 +881,9 @@ if($step < 3 || $step==4){ # don't check for step=3=clustering (not necessary) a</td>

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<td class="old_line diff-line-num" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

858

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<td class="new_line diff-line-num" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

881

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<pre style="margin: 0;"> <span id="LC881" class="line" lang="perl"><span class="nv" style="color: #008080;">@files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

859

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<td class="new_line diff-line-num" data-linenumber="882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

882

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<pre style="margin: 0;"> <span id="LC882" class="line" lang="perl"><span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">sort</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$a</span><span class="p">}</span> <span class="o" style="font-weight: 600;">==</span> <span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$b</span><span class="p">})</span> <span class="p">{</span><span class="nv" style="color: #008080;">$a</span> <span class="ow" style="font-weight: 600;">cmp</span> <span class="nv" style="color: #008080;">$b</span><span class="p">;}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$b</span><span class="p">}</span> <span class="o" style="font-weight: 600;"><=></span> <span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$a</span><span class="p">};}</span> <span class="p">}</span> <span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: #008080;">%gene_counter</span><span class="p">)</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: #008080;">@files</span><span class="p">,</span><span class="nv" style="color: #008080;">$file</span><span class="p">);}</span> <span class="c1" style="color: #998; font-style: italic;"># Biggest first # Alphabet otherwise 5.16</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

860

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<td class="new_line diff-line-num" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

883

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<pre style="margin: 0;"> <span id="LC883" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

884

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<pre style="margin: 0;">+<span id="LC884" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># 6.0.32 check if there are _clean files available -> use it instead. </span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

885

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<pre style="margin: 0;">+<span id="LC885" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">4</span><span class="p">){</span> <span class="vg" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">search_clean_file</span><span class="p">(</span><span class="vg" style="color: #008080;">$_</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="nv" style="color: #008080;">@files</span><span class="p">;</span> <span class="nv" style="color: #008080;">@files</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">uniq</span> <span class="nv" style="color: #008080;">@files</span> <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

886

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC886" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

861

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<td class="new_line diff-line-num" data-linenumber="887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

887

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<pre style="margin: 0;"> <span id="LC887" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$isoform</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">found </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: #008080;">%isoform_mapping</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> isoforms in total.</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

862

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<td class="new_line diff-line-num" data-linenumber="888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

888

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<pre style="margin: 0;"> <span id="LC888" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: #008080;">%isoform_mapping</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$isoform</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">!!!!</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">WARNING</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">!!!!</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> I did not found any isoforms as expected from the --isoform= option, please check your input data!</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Proceeding anyway...</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

863

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<td class="new_line diff-line-num" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

889

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC889" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -971,8 +997,8 @@ our @hmm_filenames;</td>

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<td class="old_line diff-line-num" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

971

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<td class="new_line diff-line-num" data-linenumber="997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

997

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<pre style="margin: 0;"> <span id="LC997" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">%hmm_filenames2colid</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

972

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<td class="new_line diff-line-num" data-linenumber="998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

998

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<pre style="margin: 0;"> <span id="LC998" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$hmm_num_cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

973

</td>

<td class="new_line diff-line-num" data-linenumber="999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

999

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<pre style="margin: 0;"> <span id="LC999" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

974

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<td class="new_line diff-line-num old" data-linenumber="1000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC974" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span>  </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

975

</td>

<td class="new_line diff-line-num old" data-linenumber="1000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC975" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$GREEN</span><span class="s2" style="color: #d14;">**Step 4**</span><span class="si" style="color: #d14;">$NC</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1000

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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$debug</span></span><span class="p">)</span> <span class="p">{</span>  </span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1001

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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$GREEN</span><span class="s2" style="color: #d14;">**Step 4<span class="idiff left right"> (experimental feature)</span>**</span><span class="si" style="color: #d14;">$NC</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

976

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<td class="new_line diff-line-num" data-linenumber="1002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1002

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<pre style="margin: 0;"> <span id="LC1002" class="line" lang="perl">  <span class="nv" style="color: #008080;">&hmmenriched</span><span class="p">;</span>             </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

977

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<td class="new_line diff-line-num" data-linenumber="1003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1003

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<pre style="margin: 0;"> <span id="LC1003" class="line" lang="perl"><span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

978

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<td class="new_line diff-line-num" data-linenumber="1004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1004

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<pre style="margin: 0;"> <span id="LC1004" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1204,7 +1230,7 @@ sub cluster {</td>

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1204

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<td class="new_line diff-line-num" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1230

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<pre style="margin: 0;"> <span id="LC1230" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1205

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<td class="new_line diff-line-num" data-linenumber="1231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1231

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<pre style="margin: 0;"> <span id="LC1231" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">system</span> <span class="p">("</span><span class="s2" style="color: #d14;">OMP_PROC_BIND=</span><span class="si" style="color: #d14;">$ompprocbind</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_clustering </span><span class="si" style="color: #d14;">$cluster_verbose_level</span><span class="s2" style="color: #d14;"> -minspecies </span><span class="si" style="color: #d14;">$minspecies</span><span class="s2" style="color: #d14;"> -ram </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$freemem_inMB</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -kmere </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">$exactstep3</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -debug </span><span class="si" style="color: #d14;">$debug</span><span class="s2" style="color: #d14;"> -cpus </span><span class="si" style="color: #d14;">$cpus</span><span class="s2" style="color: #d14;"> -weighted 1 -conn </span><span class="si" style="color: #d14;">$connectivity</span><span class="s2" style="color: #d14;"> -purity </span><span class="si" style="color: #d14;">$purity</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$clusterOptions</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""</span> <span class="p">?</span> <span class="p">"</span><span class="si" style="color: #d14;">$clusterOptions</span><span class="p">"</span> <span class="p">:</span> <span class="p">""</span> <span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -rmgraph '</span><span class="si" style="color: #d14;">$rm_simgraph</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$simgraph</span><span class="s2" style="color: #d14;">'* >'</span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">' </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="p">?</span> <span class="p">""</span> <span class="p">:</span> <span class="p">"</span><span class="s2" style="color: #d14;">2>/dev/null</span><span class="p">"));</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1206

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<td class="new_line diff-line-num" data-linenumber="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1232

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<pre style="margin: 0;"> <span id="LC1232" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1207

</td>

<td class="new_line diff-line-num old" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1207" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">[<span class="idiff left">WARNING]</span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="s2" style="color: #d14;"> proteinortho_clustering<span class="idiff"> failed. I will now retry without the OMP_PROC_BIND flag.</span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="p"><span class="idiff">";}</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># minimum 5 MB</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1233

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1233" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">[<span class="idiff left">NOTE]</span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="s2" style="color: #d14;"><span class="idiff"> I restart</span> proteinortho_clustering<span class="idiff">, it seems like the OMP_PROC_BIND flag is not compatible with the system (this has no effect on the output)</span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="p"><span class="idiff">";}</span></span><span class="idiff right"> </span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1208

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<td class="new_line diff-line-num" data-linenumber="1234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1234

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<pre style="margin: 0;"> <span id="LC1234" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span> <span class="p">("</span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_clustering </span><span class="si" style="color: #d14;">$cluster_verbose_level</span><span class="s2" style="color: #d14;"> -minspecies </span><span class="si" style="color: #d14;">$minspecies</span><span class="s2" style="color: #d14;"> -ram </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$freemem_inMB</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -kmere </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">$exactstep3</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -debug </span><span class="si" style="color: #d14;">$debug</span><span class="s2" style="color: #d14;"> -cpus </span><span class="si" style="color: #d14;">$cpus</span><span class="s2" style="color: #d14;"> -weighted 1 -conn </span><span class="si" style="color: #d14;">$connectivity</span><span class="s2" style="color: #d14;"> -purity </span><span class="si" style="color: #d14;">$purity</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$clusterOptions</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""</span> <span class="p">?</span> <span class="p">"</span><span class="si" style="color: #d14;">$clusterOptions</span><span class="p">"</span> <span class="p">:</span> <span class="p">""</span> <span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -rmgraph '</span><span class="si" style="color: #d14;">$rm_simgraph</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$simgraph</span><span class="s2" style="color: #d14;">'* >'</span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">' </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="p">?</span> <span class="p">""</span> <span class="p">:</span> <span class="p">"</span><span class="s2" style="color: #d14;">2>/dev/null</span><span class="p">"));</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1209

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<td class="new_line diff-line-num" data-linenumber="1235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1235

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<pre style="margin: 0;"> <span id="LC1235" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1210

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<td class="new_line diff-line-num" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1236

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<pre style="margin: 0;"> <span id="LC1236" class="line" lang="perl">        <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">'proteinortho_clustering' failed with code $?.</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Maybe your operating system does not support the statically compiled version, please try recompiling proteinortho with 'make clean' and 'make' (and 'make install PREFIX=...').</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1222,7 +1248,7 @@ sub cluster {</td>

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<td class="old_line diff-line-num" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1222

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<td class="new_line diff-line-num" data-linenumber="1248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1248" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1223

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<td class="new_line diff-line-num" data-linenumber="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1249" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[OUTPUT] -> Orthologous groups are written to </span><span class="si" style="color: #d14;">$simtable</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1224

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<td class="new_line diff-line-num" data-linenumber="1250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1250

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<pre style="margin: 0;"> <span id="LC1250" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@files</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">10</span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="1251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1225" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">You can extract the fasta files of each orthology group with</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">proteinortho_grab_proteins.pl </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$isoform</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""</span> <span class="p">?</span> <span class="p">"</span><span class="s2" style="color: #d14;">--isoform</span><span class="p">"</span> <span class="p">:</span> <span class="p">"")</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"><span class="idiff left right"> </span>-tofiles </span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;"> '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;">' '</span><span class="p">",</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> (Careful: This will generate a file foreach line in the file </span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">).</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1251" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">You can extract the fasta files of each orthology group with</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">proteinortho_grab_proteins.pl </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$isoform</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""</span> <span class="p">?</span> <span class="p">"</span><span class="s2" style="color: #d14;">--isoform<span class="idiff left right"> </span></span><span class="p">"</span> <span class="p">:</span> <span class="p">"")</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">-tofiles </span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;"> '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;">' '</span><span class="p">",</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> (Careful: This will generate a file foreach line in the file </span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">).</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1226

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<td class="new_line diff-line-num" data-linenumber="1252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1252

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1252" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1253

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1253" class="line" lang="perl"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1228

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<td class="new_line diff-line-num" data-linenumber="1254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1254

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1254" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">(head -n 1 '</span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">' && tail -n +2 '</span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">' | LC_ALL=C sort -k1,1nr -k2,2nr -k3,3nr ) > '</span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">.sort'; mv '</span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">.sort' '</span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">'</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1273,9 +1299,9 @@ sub cluster {</td>

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<td class="old_line diff-line-num" data-linenumber="1273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1273

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<td class="new_line diff-line-num" data-linenumber="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1299

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<pre style="margin: 0;"> <span id="LC1299" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1274

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<td class="new_line diff-line-num" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1300" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span> <span class="p">("</span><span class="s2" style="color: #d14;">OMP_PROC_BIND=</span><span class="si" style="color: #d14;">$ompprocbind</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_clustering </span><span class="si" style="color: #d14;">$cluster_verbose_level</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$clusterOptions</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""</span> <span class="p">?</span> <span class="p">"</span><span class="si" style="color: #d14;">$clusterOptions</span><span class="p">"</span> <span class="p">:</span> <span class="p">""</span> <span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -minspecies </span><span class="si" style="color: #d14;">$minspecies</span><span class="s2" style="color: #d14;"> -ram </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$freemem_inMB</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -kmere </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">$exactstep3</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -debug </span><span class="si" style="color: #d14;">$debug</span><span class="s2" style="color: #d14;"> -cpus </span><span class="si" style="color: #d14;">$cpus</span><span class="s2" style="color: #d14;"> -weighted 1 -conn </span><span class="si" style="color: #d14;">$connectivity</span><span class="s2" style="color: #d14;"> -purity </span><span class="si" style="color: #d14;">$purity</span><span class="s2" style="color: #d14;"> -rmgraph '</span><span class="si" style="color: #d14;">$rm_syngraph</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$syngraph</span><span class="s2" style="color: #d14;">'* >'</span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;">' </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="p">?</span> <span class="p">""</span> <span class="p">:</span> <span class="p">"</span><span class="s2" style="color: #d14;">2>/dev/null</span><span class="p">"));</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1275

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<td class="new_line diff-line-num" data-linenumber="1301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1301

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<pre style="margin: 0;"> <span id="LC1301" class="line" lang="perl">      </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1276

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<td class="new_line diff-line-num old" data-linenumber="1302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1276" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">[<span class="idiff left">WARNING]</span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="s2" style="color: #d14;"> proteinortho_clustering<span class="idiff"> failed. I will now retry without the OMP_PROC_BIND flag.</span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="p"><span class="idiff">";}</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># minimum 5 MB</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1302

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<pre style="margin: 0;">+<span id="LC1302" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">[<span class="idiff left">NOTE]</span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="s2" style="color: #d14;"><span class="idiff"> I restart</span> proteinortho_clustering<span class="idiff">, it seems like the OMP_PROC_BIND flag is not compatible with the system (this has no effect on the output)</span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="p"><span class="idiff">";}</span></span><span class="idiff right"> </span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1277

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<td class="new_line diff-line-num" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1303

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<pre style="margin: 0;"> <span id="LC1303" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1278

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<td class="new_line diff-line-num old" data-linenumber="1304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1278" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">[<span class="idiff left">WARNING]</span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="s2" style="color: #d14;"> proteinortho_clustering<span class="idiff"> failed. I will now retry without the OMP_PROC_BIND flag.</span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="p"><span class="idiff">";}</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># minimum 5 MB</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1304

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<pre style="margin: 0;">+<span id="LC1304" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">[<span class="idiff left">NOTE]</span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="s2" style="color: #d14;"><span class="idiff"> I restart</span> proteinortho_clustering<span class="idiff">, it seems like the OMP_PROC_BIND flag is not compatible with the system (this has no effect on the output)</span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="p"><span class="idiff">";}</span></span><span class="idiff right"> </span></span>

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<td class="old_line diff-line-num" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1279

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<td class="new_line diff-line-num" data-linenumber="1305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1305" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">system</span> <span class="p">("</span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_clustering </span><span class="si" style="color: #d14;">$cluster_verbose_level</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$clusterOptions</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""</span> <span class="p">?</span> <span class="p">"</span><span class="si" style="color: #d14;">$clusterOptions</span><span class="p">"</span> <span class="p">:</span> <span class="p">""</span> <span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -minspecies </span><span class="si" style="color: #d14;">$minspecies</span><span class="s2" style="color: #d14;"> -ram </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$freemem_inMB</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -kmere </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">$exactstep3</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -debug </span><span class="si" style="color: #d14;">$debug</span><span class="s2" style="color: #d14;"> -cpus </span><span class="si" style="color: #d14;">$cpus</span><span class="s2" style="color: #d14;"> -weighted 1 -conn </span><span class="si" style="color: #d14;">$connectivity</span><span class="s2" style="color: #d14;"> -purity </span><span class="si" style="color: #d14;">$purity</span><span class="s2" style="color: #d14;"> -rmgraph '</span><span class="si" style="color: #d14;">$rm_syngraph</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$syngraph</span><span class="s2" style="color: #d14;">'* >'</span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;">' </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="p">?</span> <span class="p">""</span> <span class="p">:</span> <span class="p">"</span><span class="s2" style="color: #d14;">2>/dev/null</span><span class="p">"));</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1280

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<td class="new_line diff-line-num" data-linenumber="1306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1306

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<pre style="margin: 0;"> <span id="LC1306" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1281

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<td class="new_line diff-line-num" data-linenumber="1307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1307

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<pre style="margin: 0;"> <span id="LC1307" class="line" lang="perl">          <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">proteinortho_clustering failed with code $?.</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Did you use a static version? Maybe your operating system does not support the static compiled version, please recompile 'make clean' and 'make' or 'make USEPRECOMPILEDLAPACK=FALSE'.</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1289,7 +1315,7 @@ sub cluster {</td>

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1289

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<td class="new_line diff-line-num" data-linenumber="1315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1315

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<pre style="margin: 0;"> <span id="LC1315" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1290

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<td class="new_line diff-line-num" data-linenumber="1316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1316

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<pre style="margin: 0;"> <span id="LC1316" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">(head -n 1 '</span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;">' && tail -n +2 '</span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;">' | LC_ALL=C sort -k1,1nr -k2,2nr -k3,3nr ) > '</span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;">.sort'; mv '</span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;">.sort' '</span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;">'</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1291

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<td class="new_line diff-line-num" data-linenumber="1317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1317

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<pre style="margin: 0;"> <span id="LC1317" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1292

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<td class="new_line diff-line-num old" data-linenumber="1318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1292" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[OUTPUT] -> Orthologous groups are written to </span><span class="si" style="color: #d14;">$syntable</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">You can extract the fasta files of each orthology group with</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">proteinortho_grab_proteins.pl </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$isoform</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""</span> <span class="p">?</span> <span class="p">"</span><span class="s2" style="color: #d14;">--isoform</span><span class="p">"</span> <span class="p">:</span> <span class="p">"")</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"><span class="idiff left right"> </span>-tofiles </span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;"> '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;">' '</span><span class="p">",</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">(Careful: This will generate a file foreach line in the file </span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;">).</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1318" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[OUTPUT] -> Orthologous groups are written to </span><span class="si" style="color: #d14;">$syntable</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">You can extract the fasta files of each orthology group with</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">proteinortho_grab_proteins.pl </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$isoform</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""</span> <span class="p">?</span> <span class="p">"</span><span class="s2" style="color: #d14;">--isoform<span class="idiff left right"> </span></span><span class="p">"</span> <span class="p">:</span> <span class="p">"")</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">-tofiles </span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;"> '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;">' '</span><span class="p">",</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">(Careful: This will generate a file foreach line in the file </span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;">).</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1319

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<pre style="margin: 0;"> <span id="LC1319" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1320" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$singles</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1321

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<pre style="margin: 0;"> <span id="LC1321" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Adding singles...</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1447,6 +1473,7 @@ Options:</td>

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<td class="old_line diff-line-num" data-linenumber="1447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1473" class="line" lang="perl"><span class="s2" style="color: #d14;">         -cov=        min. coverage of best blast alignments in % [default: 50]</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1448

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<td class="new_line diff-line-num" data-linenumber="1474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1474

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<pre style="margin: 0;"> <span id="LC1474" class="line" lang="perl"><span class="s2" style="color: #d14;">         -subparaBlast=    additional parameters for the search tool</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1475" class="line" lang="perl"><span class="s2" style="color: #d14;">                      example -subparaBlast='-seg no' or -subparaBlast='--more-sensitive' for diamond</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1476

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1476" class="line" lang="perl"><span class="s2" style="color: #d14;">         -subparaMakeBlast=    additional parameters for the database generation</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1450

</td>

<td class="new_line diff-line-num" data-linenumber="1477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1477

</td>

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<pre style="margin: 0;"> <span id="LC1477" class="line" lang="perl"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1451

</td>

<td class="new_line diff-line-num" data-linenumber="1478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1478

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<pre style="margin: 0;"> <span id="LC1478" class="line" lang="perl"><span class="s2" style="color: #d14;">         [Synteny options]</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1452

</td>

<td class="new_line diff-line-num" data-linenumber="1479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1479

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<pre style="margin: 0;"> <span id="LC1479" class="line" lang="perl"><span class="s2" style="color: #d14;">         -synteny     activate PoFF extension to separate similar sequences print</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1902,7 +1929,7 @@ sub synteny_matches {</td>

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<td class="old_line diff-line-num" data-linenumber="1902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1902

</td>

<td class="new_line diff-line-num" data-linenumber="1929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1929

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<pre style="margin: 0;"> <span id="LC1929" class="line" lang="perl"><span class="s1" style="color: #d14;">  my %track;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1903

</td>

<td class="new_line diff-line-num" data-linenumber="1930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1930

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<pre style="margin: 0;"> <span id="LC1930" class="line" lang="perl"><span class="s1" style="color: #d14;">  for my $file ($file_i, $file_j) {</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1904

</td>

<td class="new_line diff-line-num" data-linenumber="1931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1931

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<pre style="margin: 0;"> <span id="LC1931" class="line" lang="perl"><span class="s1" style="color: #d14;">    # Get Coordinates for all genes</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1905

</td>

<td class="new_line diff-line-num old" data-linenumber="1932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1905" class="line" lang="perl"><span class="s1" style="color: #d14;">    my %coords = %{&read_details($file)};</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1932

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<pre style="margin: 0;">+<span id="LC1932" class="line" lang="perl"><span class="s1" style="color: #d14;">    my %coords = %{&read_details($file<span class="idiff left right">,1</span>)};</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1906

</td>

<td class="new_line diff-line-num" data-linenumber="1933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1933

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<pre style="margin: 0;"> <span id="LC1933" class="line" lang="perl"><span class="s1" style="color: #d14;">    my $counter = 0;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1907

</td>

<td class="new_line diff-line-num" data-linenumber="1934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1934

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<pre style="margin: 0;"> <span id="LC1934" class="line" lang="perl"><span class="s1" style="color: #d14;">    # Number them according to their order</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1908

</td>

<td class="new_line diff-line-num" data-linenumber="1935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1935

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<pre style="margin: 0;"> <span id="LC1935" class="line" lang="perl"><span class="s1" style="color: #d14;">    foreach my $id (sort</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2191,6 +2218,7 @@ sub auto_cpus {</td>

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<td class="old_line diff-line-num" data-linenumber="2191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2191

</td>

<td class="new_line diff-line-num" data-linenumber="2218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2218

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<pre style="margin: 0;"> <span id="LC2218" class="line" lang="perl"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2192

</td>

<td class="new_line diff-line-num" data-linenumber="2219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2219

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<pre style="margin: 0;"> <span id="LC2219" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">generate_indices</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2193

</td>

<td class="new_line diff-line-num" data-linenumber="2220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2220

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<pre style="margin: 0;"> <span id="LC2220" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$oldkeep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$keep</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2221

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2221" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$cmd</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="2194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2194

</td>

<td class="new_line diff-line-num" data-linenumber="2222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2222

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<pre style="margin: 0;"> <span id="LC2222" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Generating indices</span><span class="p">";</span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$force</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;"> anyway (forced).</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="p">";}}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2195

</td>

<td class="new_line diff-line-num" data-linenumber="2223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2223

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<pre style="margin: 0;"> <span id="LC2223" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">rapsearch</span><span class="p">")</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num" data-linenumber="2224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2224" class="line" lang="perl">    <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">@</span><span class="nv" style="color: #008080;">_</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2198,15 +2226,15 @@ sub generate_indices {</td>

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<td class="old_line diff-line-num" data-linenumber="2198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="2226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2226" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

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<td class="old_line diff-line-num" data-linenumber="2199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="2227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2227" class="line" lang="perl">      <span class="p">}</span><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="2200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2200

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<td class="new_line diff-line-num" data-linenumber="2228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2228" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2201

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<td class="new_line diff-line-num old" data-linenumber="2229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2201" class="line" lang="perl">        <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">(</span>"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> -d '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -n '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'<span class="idiff"> ></span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/dev</span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/null</span></span><span class="p"><span class="idiff right">")</span>;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="2229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2202" class="line" lang="perl">        <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="vg" style="color: #008080;"><span class="idiff">$?</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="k" style="font-weight: 600;"><span class="idiff">print</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">STDERR</span></span><span class="idiff"> </span><span class="p"><span class="idiff">("</span></span><span class="si" style="color: #d14;"><span class="idiff">$ORANGE</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">[WARNING]</span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">$blastmode</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff"> failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in </span></span><span class="si" style="color: #d14;"><span class="idiff">$tmp_path</span></span><span class="s2" style="color: #d14;"><span class="idiff"> (-tmp).</span></span><span class="p"><span class="idiff">");</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$step</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">){</span></span><span class="k" style="font-weight: 600;"><span class="idiff">print</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">STDERR</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$ORANGE</span></span><span class="s2" style="color: #d14;"><span class="idiff"> Please ensure that you use -tmp=</span></span><span class="si" style="color: #d14;"><span class="idiff">$tmp_path</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -keep (and use the same -project= name) for future analysis.</span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="p"><span class="idiff">";}</span></span><span class="k" style="font-weight: 600;"><span class="idiff">print</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="p"><span class="idiff right">"</span>;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2203" class="line" lang="perl"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="2229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2229" class="line" lang="perl">        <span class="nv" style="color: #008080;"><span class="idiff left">$cmd</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> -d '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -n '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'</span><span class="p"><span class="idiff right">"</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2230" class="line" lang="perl">        <span class="k" style="font-weight: 600;"><span class="idiff left">my</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$makedb_ret</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">`</span></span><span class="si" style="color: #d14;"><span class="idiff">$cmd</span></span><span class="sb" style="color: #d14;"><span class="idiff"> 3>&1 1>&2 2>&3</span></span><span class="p"><span class="idiff right">`</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2231" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database (</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> -d '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -n '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'). The output is:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$makedb_ret</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2204

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<td class="new_line diff-line-num" data-linenumber="2232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2232

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<pre style="margin: 0;"> <span id="LC2232" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">mkdir</span><span class="p">("</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2205

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<td class="new_line diff-line-num" data-linenumber="2233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2233

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<pre style="margin: 0;"> <span id="LC2233" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$keep</span><span class="p">;</span><span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2206

</td>

<td class="new_line diff-line-num old" data-linenumber="2234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2206" class="line" lang="perl">          <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">(</span>"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> -d '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -n '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'<span class="idiff"> ></span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/dev</span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/null</span></span><span class="p"><span class="idiff right">")</span>;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2207

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<td class="new_line diff-line-num old" data-linenumber="2234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2207" class="line" lang="perl">          <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">ln -s '</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">abs_path</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">' '</span></span><span class="si" style="color: #d14;"><span class="idiff">$tmp_path</span></span><span class="s2" style="color: #d14;"><span class="idiff">/DB/</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">basename</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">'</span></span><span class="p"><span class="idiff right">")</span>;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2208

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<td class="new_line diff-line-num old" data-linenumber="2234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2208" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2209

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<td class="new_line diff-line-num old" data-linenumber="2234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2209" class="line" lang="perl">          <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="vg" style="color: #008080;"><span class="idiff">$?</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">){</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$keep</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nv" style="color: #008080;"><span class="idiff">$oldkeep</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">&Error</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">The database generation failed once again, please retry with 'sudo' or move the fasta files to a directory with write permissions. If this fails too, then there is something wrong with the fasta files or the version of </span></span><span class="si" style="color: #d14;"><span class="idiff">$blastmode</span></span><span class="s2" style="color: #d14;"><span class="idiff"> cannot handle the database generation. So please try one of the following:</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">- update </span></span><span class="si" style="color: #d14;"><span class="idiff">$blastmode</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">- consider another blast algorithm (-p)</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">- consider to submitting (mailing) this case to incoming+paulklemm-phd-proteinortho-7278443-issue-</span></span><span class="se" style="color: #d14;"><span class="idiff">\@</span></span><span class="s2" style="color: #d14;"><span class="idiff">incoming.gitlab.com.</span></span><span class="p">");<span class="idiff right">}</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2234

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<pre style="margin: 0;">+<span id="LC2234" class="line" lang="perl">          <span class="nv" style="color: #008080;"><span class="idiff left">$cmd</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> -d '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -n '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'</span><span class="p"><span class="idiff right">"</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2235

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<pre style="margin: 0;">+<span id="LC2235" class="line" lang="perl">          <span class="nv" style="color: #008080;"><span class="idiff left">$makedb_ret</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">`</span></span><span class="si" style="color: #d14;"><span class="idiff">$cmd</span></span><span class="sb" style="color: #d14;"><span class="idiff"> 3>&1 1>&2 2>&3</span></span><span class="p"><span class="idiff right">`</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2236

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<pre style="margin: 0;">+<span id="LC2236" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span> <span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="p">;</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">The database generation failed once again, please investigate the output from above. There is probably something wrong with the fasta files or the version of </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> cannot handle the database generation. So please try one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- update </span><span class="si" style="color: #d14;">$blastmode</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider another blast algorithm (-p)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- send this issue to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">incoming.gitlab.com.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2237

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<pre style="margin: 0;">+<span id="LC2237" class="line" lang="perl">          <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">ln -s '</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">abs_path</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">' '</span></span><span class="si" style="color: #d14;"><span class="idiff">$tmp_path</span></span><span class="s2" style="color: #d14;"><span class="idiff">/DB/</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">basename</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff right">' 2>/dev/null</span></span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2210

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<td class="new_line diff-line-num" data-linenumber="2238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2238

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<pre style="margin: 0;"> <span id="LC2238" class="line" lang="perl">        <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2211

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<td class="new_line diff-line-num" data-linenumber="2239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2239

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<pre style="margin: 0;"> <span id="LC2239" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2212

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<td class="new_line diff-line-num" data-linenumber="2240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2240

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<pre style="margin: 0;"> <span id="LC2240" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2217,15 +2245,20 @@ sub generate_indices {</td>

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<td class="old_line diff-line-num" data-linenumber="2217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2217

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<td class="new_line diff-line-num" data-linenumber="2245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2245

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<pre style="margin: 0;"> <span id="LC2245" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2218

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<td class="new_line diff-line-num" data-linenumber="2246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2246

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<pre style="margin: 0;"> <span id="LC2246" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2219

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<td class="new_line diff-line-num" data-linenumber="2247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2247

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<pre style="margin: 0;"> <span id="LC2247" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2220

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<td class="new_line diff-line-num old" data-linenumber="2248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2220" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -d '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' --quiet ></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null 2></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2221

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<td class="new_line diff-line-num old" data-linenumber="2248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2221" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2222

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<td class="new_line diff-line-num old" data-linenumber="2248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2222" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2248

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<pre style="margin: 0;">+<span id="LC2248" class="line" lang="perl">        <span class="nv" style="color: #008080;">$cmd</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -d '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' --quiet</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2249" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$makedb_ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="si" style="color: #d14;">$cmd</span><span class="sb" style="color: #d14;"> 3>&1 1>&2 2>&3</span><span class="p">`;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2250" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$makedb_ret</span> <span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">/--ignore-warnings/</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2251

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<pre style="margin: 0;">+<span id="LC2251" class="line" lang="perl">          <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database (</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -d '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'). The output is:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$makedb_ret</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">I will now retry with the '--ignore-warnings' option!</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2252

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<pre style="margin: 0;">+<span id="LC2252" class="line" lang="perl">          <span class="nv" style="color: #008080;">$cmd</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -d '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' --quiet</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2253

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<pre style="margin: 0;">+<span id="LC2253" class="line" lang="perl">          <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$makedb_ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="si" style="color: #d14;">$cmd</span><span class="sb" style="color: #d14;"> --ignore-warnings 3>&1 1>&2 2>&3</span><span class="p">`;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2254

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<pre style="margin: 0;">+<span id="LC2254" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span> <span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="p">;</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">The database generation failed once again, please investigate the output from above. There is probably something wrong with the fasta files or the version of </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> cannot handle the database generation. So please try one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- update </span><span class="si" style="color: #d14;">$blastmode</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider another blast algorithm (-p)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- send this issue to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">incoming.gitlab.com.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2255

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<pre style="margin: 0;">+<span id="LC2255" class="line" lang="perl">        <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database (</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -d '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'). The output is:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$makedb_ret</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2223

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<td class="new_line diff-line-num" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2256

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<pre style="margin: 0;"> <span id="LC2256" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">mkdir</span><span class="p">("</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2224

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<td class="new_line diff-line-num" data-linenumber="2257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2257

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<pre style="margin: 0;"> <span id="LC2257" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$keep</span><span class="p">;</span><span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2225

</td>

<td class="new_line diff-line-num old" data-linenumber="2258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2225" class="line" lang="perl">          <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">(</span>"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -d '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' --quiet<span class="idiff"> ></span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/dev</span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/null 2></span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/dev</span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/null</span></span><span class="p"><span class="idiff right">")</span>;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2226

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<td class="new_line diff-line-num old" data-linenumber="2258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2226" class="line" lang="perl">          <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">ln -s '</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">abs_path</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">' '</span></span><span class="si" style="color: #d14;"><span class="idiff">$tmp_path</span></span><span class="s2" style="color: #d14;"><span class="idiff">/DB/</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">basename</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">'</span></span><span class="p"><span class="idiff right">")</span>;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2227

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<td class="new_line diff-line-num old" data-linenumber="2258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2227" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2228

</td>

<td class="new_line diff-line-num old" data-linenumber="2258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2228" class="line" lang="perl">          <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="vg" style="color: #008080;"><span class="idiff">$?</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">){</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$keep</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nv" style="color: #008080;"><span class="idiff">$oldkeep</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">&Error</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">The database generation failed once again, please retry with 'sudo' or move the fasta files to a directory with write permissions. If this fails too, then there is something wrong with the fasta files or the version of </span></span><span class="si" style="color: #d14;"><span class="idiff">$blastmode</span></span><span class="s2" style="color: #d14;"><span class="idiff"> cannot handle the database generation. So please try one of the following:</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">- update </span></span><span class="si" style="color: #d14;"><span class="idiff">$blastmode</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">- consider another blast algorithm (-p)</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">- consider to submitting (mailing) this case to incoming+paulklemm-phd-proteinortho-7278443-issue-</span></span><span class="se" style="color: #d14;"><span class="idiff">\@</span></span><span class="s2" style="color: #d14;"><span class="idiff">incoming.gitlab.com.</span></span><span class="p">");<span class="idiff right">}</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2258

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<pre style="margin: 0;">+<span id="LC2258" class="line" lang="perl">          <span class="nv" style="color: #008080;"><span class="idiff left">$cmd</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -d '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' --quiet</span><span class="p"><span class="idiff right">"</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2259

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<pre style="margin: 0;">+<span id="LC2259" class="line" lang="perl">          <span class="nv" style="color: #008080;"><span class="idiff left">$makedb_ret</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">`</span></span><span class="si" style="color: #d14;"><span class="idiff">$cmd</span></span><span class="sb" style="color: #d14;"><span class="idiff"> 3>&1 1>&2 2>&3</span></span><span class="p"><span class="idiff right">`</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2260

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<pre style="margin: 0;">+<span id="LC2260" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span> <span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="p">;</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">The database generation failed once again, please investigate the output from above. There is probably something wrong with the fasta files or the version of </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> cannot handle the database generation. So please try one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- update </span><span class="si" style="color: #d14;">$blastmode</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider another blast algorithm (-p)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- send this issue to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">incoming.gitlab.com.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2261

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2261" class="line" lang="perl">          <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">ln -s '</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">abs_path</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">' '</span></span><span class="si" style="color: #d14;"><span class="idiff">$tmp_path</span></span><span class="s2" style="color: #d14;"><span class="idiff">/DB/</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">basename</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff right">' 2>/dev/null</span></span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2229

</td>

<td class="new_line diff-line-num" data-linenumber="2262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2262

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2262" class="line" lang="perl">        <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2230

</td>

<td class="new_line diff-line-num" data-linenumber="2263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2263

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2263" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2231

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<td class="new_line diff-line-num" data-linenumber="2264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2264

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2264" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2234,20 +2267,20 @@ sub generate_indices {</td>

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<td class="old_line diff-line-num" data-linenumber="2234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2234

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<td class="new_line diff-line-num" data-linenumber="2267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2267

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2267" class="line" lang="perl">    <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">@</span><span class="nv" style="color: #008080;">_</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2235

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<td class="new_line diff-line-num" data-linenumber="2268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2268

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2268" class="line" lang="perl">        <span class="c1" style="color: #998; font-style: italic;">#if ($file =~ /\s/) {print STDERR ("$ORANGE\n[WARNING]$NC : File name '$file' contains whitespaces. This might lead to undesired effects. If you encounter unusual behavior, please change the file name!$NC\n");}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2236

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<td class="new_line diff-line-num" data-linenumber="2269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2269

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2269" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2237

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<td class="new_line diff-line-num old" data-linenumber="2270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2237" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2238

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<td class="new_line diff-line-num" data-linenumber="2270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2270

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2270" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 2>/dev/null</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2239

</td>

<td class="new_line diff-line-num" data-linenumber="2271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2271

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2271" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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

<td class="old_line diff-line-num" data-linenumber="2240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2240

</td>

<td class="new_line diff-line-num" data-linenumber="2272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2272

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2272" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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

<td class="old_line diff-line-num" data-linenumber="2241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2241

</td>

<td class="new_line diff-line-num" data-linenumber="2273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2273

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2273" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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

<td class="old_line diff-line-num old" data-linenumber="2242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2242

</td>

<td class="new_line diff-line-num old" data-linenumber="2274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2242" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> index -f '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -p '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null 2></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="2243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2243

</td>

<td class="new_line diff-line-num old" data-linenumber="2274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2243" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="2244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2274

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2274" class="line" lang="perl">        <span class="nv" style="color: #008080;">$cmd</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> index -f '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -p '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'</span><span class="p">";</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="2244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2275

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2275" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$makedb_ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="si" style="color: #d14;">$cmd</span><span class="sb" style="color: #d14;"> 3>&1 1>&2 2>&3</span><span class="p">`;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2276

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2276" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database (</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> index -f '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -p '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'). The output is:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$makedb_ret</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2244

</td>

<td class="new_line diff-line-num" data-linenumber="2277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2277

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2277" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2245

</td>

<td class="new_line diff-line-num" data-linenumber="2278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2278

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2278" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">mkdir</span><span class="p">("</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB</span><span class="p">");</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2246

</td>

<td class="new_line diff-line-num" data-linenumber="2279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2279

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2279" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$keep</span><span class="p">;</span><span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2247

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<td class="new_line diff-line-num old" data-linenumber="2280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2247" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> index -f '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -p '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null 2></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2280

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<pre style="margin: 0;">+<span id="LC2280" class="line" lang="perl">          <span class="nv" style="color: #008080;">$cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> index -f '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -p '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2281

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<pre style="margin: 0;">+<span id="LC2281" class="line" lang="perl">          <span class="nv" style="color: #008080;">$makedb_ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="si" style="color: #d14;">$cmd</span><span class="sb" style="color: #d14;"> 3>&1 1>&2 2>&3</span><span class="p">`;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2282

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<pre style="margin: 0;">+<span id="LC2282" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span> <span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="p">;</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">The database generation failed once again, please investigate the output from above. There is probably something wrong with the fasta files or the version of </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> cannot handle the database generation. So please try one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- update </span><span class="si" style="color: #d14;">$blastmode</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider another blast algorithm (-p)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- send this issue to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">incoming.gitlab.com.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2248

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<td class="new_line diff-line-num" data-linenumber="2283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2283

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<pre style="margin: 0;"> <span id="LC2283" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">ln -s '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">abs_path</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">'</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2249

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<td class="new_line diff-line-num old" data-linenumber="2284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2249" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2250

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<td class="new_line diff-line-num old" data-linenumber="2284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2250" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span> <span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="p">;</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">The database generation failed once again, please retry with 'sudo' or move the fasta files to a directory with write permissions. If this fails too, then there is something wrong with the fasta files or the version of </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> cannot handle the database generation. So please try one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- update </span><span class="si" style="color: #d14;">$blastmode</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider another blast algorithm (-p)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider to submitting (mailing) this case to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">incoming.gitlab.com.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2251

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<td class="new_line diff-line-num" data-linenumber="2284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2284

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<pre style="margin: 0;"> <span id="LC2284" class="line" lang="perl">        <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2252

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<td class="new_line diff-line-num" data-linenumber="2285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2285

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<pre style="margin: 0;"> <span id="LC2285" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="2286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2286

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<pre style="margin: 0;"> <span id="LC2286" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2258,15 +2291,16 @@ sub generate_indices {</td>

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<td class="new_line diff-line-num" data-linenumber="2291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2291

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<pre style="margin: 0;"> <span id="LC2291" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="2292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2292

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<pre style="margin: 0;"> <span id="LC2292" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2260

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<td class="new_line diff-line-num" data-linenumber="2293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2293

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<pre style="margin: 0;"> <span id="LC2293" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2261

</td>

<td class="new_line diff-line-num old" data-linenumber="2294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2261" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> --dbtype 1 '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null 2></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2262

</td>

<td class="new_line diff-line-num old" data-linenumber="2294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2262" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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

<td class="old_line diff-line-num new" data-linenumber="2263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2294

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2294" class="line" lang="perl">        <span class="nv" style="color: #008080;">$cmd</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> --dbtype 1 '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'</span><span class="p">";</span></span>

</pre>

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

<td class="old_line diff-line-num new" data-linenumber="2263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2295

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2295" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$makedb_ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="si" style="color: #d14;">$cmd</span><span class="sb" style="color: #d14;"> 3>&1 1>&2 2>&3</span><span class="p">`;</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="2263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2296

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2296" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database (</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> --dbtype 1 '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'). The output is:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$makedb_ret</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2263

</td>

<td class="new_line diff-line-num" data-linenumber="2297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2297

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2297" class="line" lang="perl"></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2264

</td>

<td class="new_line diff-line-num" data-linenumber="2298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2298

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2298" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">mkdir</span><span class="p">("</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB</span><span class="p">");</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2265

</td>

<td class="new_line diff-line-num" data-linenumber="2299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2299

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2299" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$keep</span><span class="p">;</span><span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2266

</td>

<td class="new_line diff-line-num old" data-linenumber="2300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2266" class="line" lang="perl">          <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">(</span>"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> --dbtype 1 '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'<span class="idiff"> ></span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/dev</span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/null 2></span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/dev</span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/null</span></span><span class="p"><span class="idiff right">")</span>;</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="2267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2267

</td>

<td class="new_line diff-line-num old" data-linenumber="2300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2267" class="line" lang="perl">          <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">ln -s '</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">abs_path</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">' '</span></span><span class="si" style="color: #d14;"><span class="idiff">$tmp_path</span></span><span class="s2" style="color: #d14;"><span class="idiff">/DB/</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">basename</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">'</span></span><span class="p"><span class="idiff right">")</span>;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2268

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<td class="new_line diff-line-num old" data-linenumber="2300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2268" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2269

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<td class="new_line diff-line-num old" data-linenumber="2300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2269" class="line" lang="perl">          <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="vg" style="color: #008080;"><span class="idiff">$?</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">){</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$keep</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nv" style="color: #008080;"><span class="idiff">$oldkeep</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">&Error</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">The database generation failed once again, please retry with 'sudo' or move the fasta files to a directory with write permissions. If this fails too, then there is something wrong with the fasta files or the version of </span></span><span class="si" style="color: #d14;"><span class="idiff">$blastmode</span></span><span class="s2" style="color: #d14;"><span class="idiff"> cannot handle the database generation. So please try one of the following:</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">- update </span></span><span class="si" style="color: #d14;"><span class="idiff">$blastmode</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">- consider another blast algorithm (-p)</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">- consider to submitting (mailing) this case to incoming+paulklemm-phd-proteinortho-7278443-issue-</span></span><span class="se" style="color: #d14;"><span class="idiff">\@</span></span><span class="s2" style="color: #d14;"><span class="idiff">incoming.gitlab.com.</span></span><span class="p">");<span class="idiff right">}</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2300

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<pre style="margin: 0;">+<span id="LC2300" class="line" lang="perl">          <span class="nv" style="color: #008080;"><span class="idiff left">$cmd</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> --dbtype 1 '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'</span><span class="p"><span class="idiff right">"</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2301

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<pre style="margin: 0;">+<span id="LC2301" class="line" lang="perl">          <span class="nv" style="color: #008080;"><span class="idiff left">$makedb_ret</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">`</span></span><span class="si" style="color: #d14;"><span class="idiff">$cmd</span></span><span class="sb" style="color: #d14;"><span class="idiff"> 3>&1 1>&2 2>&3</span></span><span class="p"><span class="idiff right">`</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2302

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<pre style="margin: 0;">+<span id="LC2302" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span> <span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="p">;</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">The database generation failed once again, please investigate the output from above. There is probably something wrong with the fasta files or the version of </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> cannot handle the database generation. So please try one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- update </span><span class="si" style="color: #d14;">$blastmode</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider another blast algorithm (-p)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- send this issue to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">incoming.gitlab.com.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2303

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<pre style="margin: 0;">+<span id="LC2303" class="line" lang="perl">          <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">ln -s '</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">abs_path</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">' '</span></span><span class="si" style="color: #d14;"><span class="idiff">$tmp_path</span></span><span class="s2" style="color: #d14;"><span class="idiff">/DB/</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">basename</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff right">' 2>/dev/null</span></span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2270

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<td class="new_line diff-line-num" data-linenumber="2304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2304

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<pre style="margin: 0;"> <span id="LC2304" class="line" lang="perl">        <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2271

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<td class="new_line diff-line-num" data-linenumber="2305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2305

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2305" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2272

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<td class="new_line diff-line-num" data-linenumber="2306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2306

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<pre style="margin: 0;"> <span id="LC2306" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2277,15 +2311,16 @@ sub generate_indices {</td>

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<td class="old_line diff-line-num" data-linenumber="2277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2277

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<td class="new_line diff-line-num" data-linenumber="2311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2311

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<pre style="margin: 0;"> <span id="LC2311" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2278

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<td class="new_line diff-line-num" data-linenumber="2312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2312

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<pre style="margin: 0;"> <span id="LC2312" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2279

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<td class="new_line diff-line-num" data-linenumber="2313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2313

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<pre style="margin: 0;"> <span id="LC2313" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2280

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<td class="new_line diff-line-num old" data-linenumber="2314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC2280" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> --dbtype 2 '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null 2></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2281

</td>

<td class="new_line diff-line-num old" data-linenumber="2314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2281" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2314

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2314" class="line" lang="perl">        <span class="nv" style="color: #008080;">$cmd</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> --dbtype 2 '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2315

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2315" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$makedb_ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="si" style="color: #d14;">$cmd</span><span class="sb" style="color: #d14;"> 3>&1 1>&2 2>&3</span><span class="p">`;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2316

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2316" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database (</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> --dbtype 2 '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'). The output is:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$makedb_ret</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2282

</td>

<td class="new_line diff-line-num" data-linenumber="2317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2317

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2317" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2283

</td>

<td class="new_line diff-line-num" data-linenumber="2318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2318

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2318" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">mkdir</span><span class="p">("</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2284

</td>

<td class="new_line diff-line-num" data-linenumber="2319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2319

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2319" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$keep</span><span class="p">;</span><span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2285

</td>

<td class="new_line diff-line-num old" data-linenumber="2320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2285" class="line" lang="perl">          <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">(</span>"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> --dbtype 2 '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'<span class="idiff"> ></span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/dev</span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/null 2></span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/dev</span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/null</span></span><span class="p"><span class="idiff right">")</span>;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2286

</td>

<td class="new_line diff-line-num old" data-linenumber="2320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2286" class="line" lang="perl">          <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">ln -s '</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">abs_path</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">' '</span></span><span class="si" style="color: #d14;"><span class="idiff">$tmp_path</span></span><span class="s2" style="color: #d14;"><span class="idiff">/DB/</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">basename</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">'</span></span><span class="p"><span class="idiff right">")</span>;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2287

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<td class="new_line diff-line-num old" data-linenumber="2320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2287" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2288

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<td class="new_line diff-line-num old" data-linenumber="2320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2288" class="line" lang="perl">          <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="vg" style="color: #008080;"><span class="idiff">$?</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">){</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$keep</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nv" style="color: #008080;"><span class="idiff">$oldkeep</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">&Error</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">The database generation failed once again, please retry with 'sudo' or move the fasta files to a directory with write permissions. If this fails too, then there is something wrong with the fasta files or the version of </span></span><span class="si" style="color: #d14;"><span class="idiff">$blastmode</span></span><span class="s2" style="color: #d14;"><span class="idiff"> cannot handle the database generation. So please try one of the following:</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">- update </span></span><span class="si" style="color: #d14;"><span class="idiff">$blastmode</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">- consider another blast algorithm (-p)</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">- consider to submitting (mailing) this case to incoming+paulklemm-phd-proteinortho-7278443-issue-</span></span><span class="se" style="color: #d14;"><span class="idiff">\@</span></span><span class="s2" style="color: #d14;"><span class="idiff">incoming.gitlab.com.</span></span><span class="p">");<span class="idiff right">}</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2320

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<pre style="margin: 0;">+<span id="LC2320" class="line" lang="perl">          <span class="nv" style="color: #008080;"><span class="idiff left">$cmd</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> --dbtype 2 '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'</span><span class="p"><span class="idiff right">"</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2321

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<pre style="margin: 0;">+<span id="LC2321" class="line" lang="perl">          <span class="nv" style="color: #008080;"><span class="idiff left">$makedb_ret</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">`</span></span><span class="si" style="color: #d14;"><span class="idiff">$cmd</span></span><span class="sb" style="color: #d14;"><span class="idiff"> 3>&1 1>&2 2>&3</span></span><span class="p"><span class="idiff right">`</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2322

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<pre style="margin: 0;">+<span id="LC2322" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span> <span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="p">;</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">The database generation failed once again, please investigate the output from above. There is probably something wrong with the fasta files or the version of </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> cannot handle the database generation. So please try one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- update </span><span class="si" style="color: #d14;">$blastmode</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider another blast algorithm (-p)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- send this issue to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">incoming.gitlab.com.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2323

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<pre style="margin: 0;">+<span id="LC2323" class="line" lang="perl">          <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">ln -s '</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">abs_path</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">' '</span></span><span class="si" style="color: #d14;"><span class="idiff">$tmp_path</span></span><span class="s2" style="color: #d14;"><span class="idiff">/DB/</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">basename</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff right">' 2>/dev/null</span></span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2289

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<td class="new_line diff-line-num" data-linenumber="2324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2324

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<pre style="margin: 0;"> <span id="LC2324" class="line" lang="perl">        <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2290

</td>

<td class="new_line diff-line-num" data-linenumber="2325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2325

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2325" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2291

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<td class="new_line diff-line-num" data-linenumber="2326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2326

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<pre style="margin: 0;"> <span id="LC2326" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2296,15 +2331,16 @@ sub generate_indices {</td>

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<td class="old_line diff-line-num" data-linenumber="2296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2296

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<td class="new_line diff-line-num" data-linenumber="2331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2331

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<pre style="margin: 0;"> <span id="LC2331" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2297

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<td class="new_line diff-line-num" data-linenumber="2332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2332

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<pre style="margin: 0;"> <span id="LC2332" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2298

</td>

<td class="new_line diff-line-num" data-linenumber="2333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2333

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<pre style="margin: 0;"> <span id="LC2333" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2299

</td>

<td class="new_line diff-line-num old" data-linenumber="2334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2299" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -output '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null 2></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2300

</td>

<td class="new_line diff-line-num old" data-linenumber="2334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2300" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2334

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2334" class="line" lang="perl">        <span class="nv" style="color: #008080;">$cmd</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -output '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'</span><span class="p">";</span></span>

</pre>

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

<td class="old_line diff-line-num new" data-linenumber="2301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2335

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2335" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$makedb_ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="si" style="color: #d14;">$cmd</span><span class="sb" style="color: #d14;"> 3>&1 1>&2 2>&3</span><span class="p">`;</span></span>

</pre>

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

<td class="old_line diff-line-num new" data-linenumber="2301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2336

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2336" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database (</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -output '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'). The output is:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$makedb_ret</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2301

</td>

<td class="new_line diff-line-num" data-linenumber="2337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2337

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2337" class="line" lang="perl"></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2302

</td>

<td class="new_line diff-line-num" data-linenumber="2338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2338

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2338" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">mkdir</span><span class="p">("</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB</span><span class="p">");</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2303

</td>

<td class="new_line diff-line-num" data-linenumber="2339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2339

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2339" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$keep</span><span class="p">;</span><span class="nv" style="color: #008080;">$keep</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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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2304

</td>

<td class="new_line diff-line-num old" data-linenumber="2340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2304" class="line" lang="perl">          <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">(</span>"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -output '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'<span class="idiff"> ></span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/dev</span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/null 2></span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/dev</span></span><span class="se" style="color: #d14;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/null</span></span><span class="p"><span class="idiff right">")</span>;</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="2305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2305

</td>

<td class="new_line diff-line-num old" data-linenumber="2340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2305" class="line" lang="perl">          <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">ln -s '</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">abs_path</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">' '</span></span><span class="si" style="color: #d14;"><span class="idiff">$tmp_path</span></span><span class="s2" style="color: #d14;"><span class="idiff">/DB/</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">basename</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">'</span></span><span class="p"><span class="idiff right">")</span>;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2306

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<pre style="margin: 0;">-<span id="LC2306" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2307

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<td class="new_line diff-line-num old" data-linenumber="2340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2307" class="line" lang="perl">          <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="vg" style="color: #008080;"><span class="idiff">$?</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">){</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$keep</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nv" style="color: #008080;"><span class="idiff">$oldkeep</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">&Error</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">The database generation failed once again, please retry with 'sudo' or move the fasta files to a directory with write permissions. If this fails too, then there is something wrong with the fasta files or the version of </span></span><span class="si" style="color: #d14;"><span class="idiff">$blastmode</span></span><span class="s2" style="color: #d14;"><span class="idiff"> cannot handle the database generation. So please try one of the following:</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">- update </span></span><span class="si" style="color: #d14;"><span class="idiff">$blastmode</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">- consider another blast algorithm (-p)</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">- consider to submitting (mailing) this case to incoming+paulklemm-phd-proteinortho-7278443-issue-</span></span><span class="se" style="color: #d14;"><span class="idiff">\@</span></span><span class="s2" style="color: #d14;"><span class="idiff">incoming.gitlab.com.</span></span><span class="p">");<span class="idiff right">}</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2340" class="line" lang="perl">          <span class="nv" style="color: #008080;"><span class="idiff left">$cmd</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -output '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'</span><span class="p"><span class="idiff right">"</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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2341

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<pre style="margin: 0;">+<span id="LC2341" class="line" lang="perl">          <span class="nv" style="color: #008080;"><span class="idiff left">$makedb_ret</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">`</span></span><span class="si" style="color: #d14;"><span class="idiff">$cmd</span></span><span class="sb" style="color: #d14;"><span class="idiff"> 3>&1 1>&2 2>&3</span></span><span class="p"><span class="idiff right">`</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2342" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span> <span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="p">;</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">The database generation failed once again, please investigate the output from above. There is probably something wrong with the fasta files or the version of </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> cannot handle the database generation. So please try one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- update </span><span class="si" style="color: #d14;">$blastmode</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider another blast algorithm (-p)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- send this issue to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">incoming.gitlab.com.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2343

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<pre style="margin: 0;">+<span id="LC2343" class="line" lang="perl">          <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">ln -s '</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">abs_path</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">' '</span></span><span class="si" style="color: #d14;"><span class="idiff">$tmp_path</span></span><span class="s2" style="color: #d14;"><span class="idiff">/DB/</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">basename</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff right">' 2>/dev/null</span></span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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2344

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<pre style="margin: 0;"> <span id="LC2344" class="line" lang="perl">        <span class="p">}</span></span>

</pre>

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2345

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<pre style="margin: 0;"> <span id="LC2345" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="2346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2346

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<pre style="margin: 0;"> <span id="LC2346" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2316,26 +2352,28 @@ sub generate_indices {</td>

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<td class="old_line diff-line-num" data-linenumber="2316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2352" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC2353" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2318

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<td class="new_line diff-line-num" data-linenumber="2354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2354

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<pre style="margin: 0;"> <span id="LC2354" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">lastp</span><span class="p">"){</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2319

</td>

<td class="new_line diff-line-num old" data-linenumber="2355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2319" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> -p '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2320

</td>

<td class="new_line diff-line-num old" data-linenumber="2355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2320" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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

<td class="old_line diff-line-num new" data-linenumber="2321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2355

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2355" class="line" lang="perl">          <span class="nv" style="color: #008080;">$cmd</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> -p '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="p">";</span></span>

</pre>

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

<td class="old_line diff-line-num new" data-linenumber="2321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2356

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2356" class="line" lang="perl">          <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$makedb_ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="si" style="color: #d14;">$cmd</span><span class="sb" style="color: #d14;"> 3>&1 1>&2 2>&3</span><span class="p">`;</span></span>

</pre>

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

<td class="old_line diff-line-num new" data-linenumber="2321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2357

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2357" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database (</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> -p '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'). The output is:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$makedb_ret</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2321

</td>

<td class="new_line diff-line-num" data-linenumber="2358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2358

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2358" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2322

</td>

<td class="new_line diff-line-num" data-linenumber="2359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2359

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2359" class="line" lang="perl">            <span class="nb" style="color: #0086b3;">mkdir</span><span class="p">("</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2323

</td>

<td class="new_line diff-line-num" data-linenumber="2360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2360

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2360" class="line" lang="perl">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$keep</span><span class="p">;</span><span class="nv" style="color: #008080;">$keep</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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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2324

</td>

<td class="new_line diff-line-num old" data-linenumber="2361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2324" class="line" lang="perl">            <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">(</span>"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> -p '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="p">"<span class="idiff right">)</span>;</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="2325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2325

</td>

<td class="new_line diff-line-num old" data-linenumber="2361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2325" class="line" lang="perl">            <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">ln -s '</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">abs_path</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">' '</span></span><span class="si" style="color: #d14;"><span class="idiff">$tmp_path</span></span><span class="s2" style="color: #d14;"><span class="idiff">/DB/</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">basename</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">'</span></span><span class="p"><span class="idiff right">")</span>;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2326

</td>

<td class="new_line diff-line-num old" data-linenumber="2361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2326" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2327

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<td class="new_line diff-line-num old" data-linenumber="2361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2327" class="line" lang="perl">            <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="vg" style="color: #008080;"><span class="idiff">$?</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">){</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">&Error</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">The database generation failed once again, please retry with 'sudo' or move the fasta files to a directory with write permissions. If this fails too, then there is }something wrong with the fasta files or the version of </span></span><span class="si" style="color: #d14;"><span class="idiff">$blastmode</span></span><span class="s2" style="color: #d14;"><span class="idiff"> cannot handle the database generation. So try to update </span></span><span class="si" style="color: #d14;"><span class="idiff">$blastmode</span></span><span class="s2" style="color: #d14;"><span class="idiff">, consider another blast algorithm (-p) or consider to submitting this case to .</span></span><span class="p">");<span class="idiff right">}</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2361

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<pre style="margin: 0;">+<span id="LC2361" class="line" lang="perl">            <span class="nv" style="color: #008080;"><span class="idiff left">$cmd</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> -p '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2362

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<pre style="margin: 0;">+<span id="LC2362" class="line" lang="perl">            <span class="nv" style="color: #008080;"><span class="idiff left">$makedb_ret</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">`</span></span><span class="si" style="color: #d14;"><span class="idiff">$cmd</span></span><span class="sb" style="color: #d14;"><span class="idiff"> 3>&1 1>&2 2>&3</span></span><span class="p"><span class="idiff right">`</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2363

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<pre style="margin: 0;">+<span id="LC2363" class="line" lang="perl">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">The database generation failed once again, please investigate the output from above. There is probably }something wrong with the fasta files or the version of </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> cannot handle the database generation. So try to update </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">, consider another blast algorithm (-p) or consider to submitting this case to .</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2364

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<pre style="margin: 0;">+<span id="LC2364" class="line" lang="perl">            <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">ln -s '</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">abs_path</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">' '</span></span><span class="si" style="color: #d14;"><span class="idiff">$tmp_path</span></span><span class="s2" style="color: #d14;"><span class="idiff">/DB/</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">basename</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff right">' 2>/dev/null</span></span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2328

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<td class="new_line diff-line-num" data-linenumber="2365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2365

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<pre style="margin: 0;"> <span id="LC2365" class="line" lang="perl">          <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2329

</td>

<td class="new_line diff-line-num" data-linenumber="2366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2366

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<pre style="margin: 0;"> <span id="LC2366" class="line" lang="perl">        <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2330

</td>

<td class="new_line diff-line-num old" data-linenumber="2367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2330" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2331

</td>

<td class="new_line diff-line-num old" data-linenumber="2367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2331" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2367

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<pre style="margin: 0;">+<span id="LC2367" class="line" lang="perl">          <span class="nv" style="color: #008080;">$cmd</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2368

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<pre style="margin: 0;">+<span id="LC2368" class="line" lang="perl">          <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$makedb_ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="si" style="color: #d14;">$cmd</span><span class="sb" style="color: #d14;"> 3>&1 1>&2 2>&3</span><span class="p">`;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2369

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<pre style="margin: 0;">+<span id="LC2369" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database (</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'). The output is:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$makedb_ret</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2332

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<td class="new_line diff-line-num" data-linenumber="2370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2370

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<pre style="margin: 0;"> <span id="LC2370" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2333

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<td class="new_line diff-line-num" data-linenumber="2371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2371

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<pre style="margin: 0;"> <span id="LC2371" class="line" lang="perl">            <span class="nb" style="color: #0086b3;">mkdir</span><span class="p">("</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2334

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<td class="new_line diff-line-num" data-linenumber="2372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2372

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<pre style="margin: 0;"> <span id="LC2372" class="line" lang="perl">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$keep</span><span class="p">;</span><span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2335

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<td class="new_line diff-line-num old" data-linenumber="2373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2335" class="line" lang="perl">            <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">(</span>"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="p">"<span class="idiff right">)</span>;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2336

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<td class="new_line diff-line-num old" data-linenumber="2373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2336" class="line" lang="perl">            <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">ln -s '</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">abs_path</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">' '</span></span><span class="si" style="color: #d14;"><span class="idiff">$tmp_path</span></span><span class="s2" style="color: #d14;"><span class="idiff">/DB/</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">basename</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">'</span></span><span class="p"><span class="idiff right">")</span>;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2337

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<td class="new_line diff-line-num old" data-linenumber="2373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2337" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2338

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<td class="new_line diff-line-num old" data-linenumber="2373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2338" class="line" lang="perl">            <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="vg" style="color: #008080;"><span class="idiff">$?</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">){</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$keep</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nv" style="color: #008080;"><span class="idiff">$oldkeep</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">&Error</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">The database generation failed once again, please retry with 'sudo' or move the fasta files to a directory with write permissions. If this fails too, then there is something wrong with the fasta files or the version of </span></span><span class="si" style="color: #d14;"><span class="idiff">$blastmode</span></span><span class="s2" style="color: #d14;"><span class="idiff"> cannot handle the database generation. So please try one of the following:</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">- update </span></span><span class="si" style="color: #d14;"><span class="idiff">$blastmode</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">- consider another blast algorithm (-p)</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">- consider to submitting (mailing) this case to incoming+paulklemm-phd-proteinortho-7278443-issue-</span></span><span class="se" style="color: #d14;"><span class="idiff">\@</span></span><span class="s2" style="color: #d14;"><span class="idiff">incoming.gitlab.com.</span></span><span class="p">");<span class="idiff right">}</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2373

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2373" class="line" lang="perl">            <span class="nv" style="color: #008080;"><span class="idiff left">$cmd</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2374

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<pre style="margin: 0;">+<span id="LC2374" class="line" lang="perl">            <span class="nv" style="color: #008080;"><span class="idiff left">$makedb_ret</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">`</span></span><span class="si" style="color: #d14;"><span class="idiff">$cmd</span></span><span class="sb" style="color: #d14;"><span class="idiff"> 3>&1 1>&2 2>&3</span></span><span class="p"><span class="idiff right">`</span>;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2375

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<pre style="margin: 0;">+<span id="LC2375" class="line" lang="perl">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span> <span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="p">;</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">The database generation failed once again, please investigate the output from above. There is probably something wrong with the fasta files or the version of </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> cannot handle the database generation. So please try one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- update </span><span class="si" style="color: #d14;">$blastmode</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider another blast algorithm (-p)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- send this issue to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">incoming.gitlab.com.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2376

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<pre style="margin: 0;">+<span id="LC2376" class="line" lang="perl">            <span class="nb" style="color: #0086b3;"><span class="idiff left">system</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">ln -s '</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">abs_path</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">' '</span></span><span class="si" style="color: #d14;"><span class="idiff">$tmp_path</span></span><span class="s2" style="color: #d14;"><span class="idiff">/DB/</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">basename</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff right">' 2>/dev/null</span></span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2339

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<td class="new_line diff-line-num" data-linenumber="2377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2377

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<pre style="margin: 0;"> <span id="LC2377" class="line" lang="perl">          <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2340

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<td class="new_line diff-line-num" data-linenumber="2378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2378

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<pre style="margin: 0;"> <span id="LC2378" class="line" lang="perl">        <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2341

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<td class="new_line diff-line-num" data-linenumber="2379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2379

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<pre style="margin: 0;"> <span id="LC2379" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2350,18 +2388,21 @@ sub generate_indices {</td>

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<td class="old_line diff-line-num" data-linenumber="2350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2350

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<td class="new_line diff-line-num" data-linenumber="2388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2388

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<pre style="margin: 0;"> <span id="LC2388" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2351

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<td class="new_line diff-line-num" data-linenumber="2389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2389

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<pre style="margin: 0;"> <span id="LC2389" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2352

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<td class="new_line diff-line-num" data-linenumber="2390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2390

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<pre style="margin: 0;"> <span id="LC2390" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2353

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<td class="new_line diff-line-num old" data-linenumber="2391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2353" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -out '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2354

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<td class="new_line diff-line-num old" data-linenumber="2391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2354" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -out '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2355

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<td class="new_line diff-line-num old" data-linenumber="2391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2355" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2391

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<pre style="margin: 0;">+<span id="LC2391" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -out '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2392

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2392" class="line" lang="perl">        <span class="nv" style="color: #008080;">$cmd</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -out '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2393

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2393" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$makedb_ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="si" style="color: #d14;">$cmd</span><span class="sb" style="color: #d14;"> 3>&1 1>&2 2>&3</span><span class="p">`;</span></span>

</pre>

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

<td class="old_line diff-line-num new" data-linenumber="2356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2394

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2394" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database (</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -out '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'). The output is:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$makedb_ret</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2356

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<td class="new_line diff-line-num" data-linenumber="2395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2395

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2395" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2357

</td>

<td class="new_line diff-line-num" data-linenumber="2396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2396

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<pre style="margin: 0;"> <span id="LC2396" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">mkdir</span><span class="p">("</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2358

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<td class="new_line diff-line-num" data-linenumber="2397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2397

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<pre style="margin: 0;"> <span id="LC2397" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$keep</span><span class="p">;</span><span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2359

</td>

<td class="new_line diff-line-num old" data-linenumber="2398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2359" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -out '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2398

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2398" class="line" lang="perl">          <span class="nv" style="color: #008080;">$cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -out '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2399

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2399" class="line" lang="perl">          <span class="nv" style="color: #008080;">$makedb_ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="si" style="color: #d14;">$cmd</span><span class="sb" style="color: #d14;"> 3>&1 1>&2 2>&3</span><span class="p">`;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2400

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2400" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">ln -s '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">abs_path</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' 2>/dev/null</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2360

</td>

<td class="new_line diff-line-num" data-linenumber="2401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2401

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2401" class="line" lang="perl"></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="2361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2361

</td>

<td class="new_line diff-line-num old" data-linenumber="2402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2361" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span> <span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="p">;</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">The database generation failed once again, please <span class="idiff left">retry with 'sudo' or move the fasta files to a directory with write permissions. If this fails too, then there is</span> something wrong with the fasta files or the version of </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> cannot handle the database generation. So please try one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- update </span><span class="si" style="color: #d14;">$blastmode</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider another blast algorithm (-p)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- <span class="idiff">consider to submitting (mailing)</span> this <span class="idiff right">cas</span>e to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">incoming.gitlab.com.</span><span class="p">");}}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2402

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2402" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span> <span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="p">;</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">The database generation failed once again, please <span class="idiff left">investigate the output from above. There is probably</span> something wrong with the fasta files or the version of </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> cannot handle the database generation. So please try one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- update </span><span class="si" style="color: #d14;">$blastmode</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider another blast algorithm (-p)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- <span class="idiff">send</span> this <span class="idiff right">issu</span>e to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">incoming.gitlab.com.</span><span class="p">");}}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2362

</td>

<td class="new_line diff-line-num" data-linenumber="2403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2403

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2403" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2363

</td>

<td class="new_line diff-line-num" data-linenumber="2404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2404

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2404" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2364

</td>

<td class="new_line diff-line-num old" data-linenumber="2405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2364" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">unlink</span><span class="p">('</span><span class="s1" style="color: #d14;">formatdb.log</span><span class="p">');</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2405

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2405" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">unlink</span><span class="p">('</span><span class="s1" style="color: #d14;">formatdb.log</span><span class="p">')</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="nv" style="color: #008080;"><span class="idiff">e</span></span><span class="idiff"> </span><span class="p"><span class="idiff">'</span></span><span class="s1" style="color: #d14;"><span class="idiff">formatdb.log</span></span><span class="p"><span class="idiff right">'</span>;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2365

</td>

<td class="new_line diff-line-num" data-linenumber="2406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2406

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2406" class="line" lang="perl">  <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/autoblast/</span><span class="p">)</span> <span class="p">{</span>  <span class="c1" style="color: #998; font-style: italic;"># new blast+</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2366

</td>

<td class="new_line diff-line-num" data-linenumber="2407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2407

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2407" class="line" lang="perl">    <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">@</span><span class="nv" style="color: #008080;">_</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2367

</td>

<td class="new_line diff-line-num" data-linenumber="2408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2408

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2408" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 2>/dev/null</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2372,36 +2413,42 @@ sub generate_indices {</td>

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<td class="old_line diff-line-num" data-linenumber="2372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2372

</td>

<td class="new_line diff-line-num" data-linenumber="2413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2413

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2413" class="line" lang="perl">          <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> I could not detect the type of '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">', i assume aminoacid sequences...</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2373

</td>

<td class="new_line diff-line-num" data-linenumber="2414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2414

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2414" class="line" lang="perl">          <span class="nv" style="color: #008080;">$autoblast_fileis</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">prot</span><span class="p">";</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2374

</td>

<td class="new_line diff-line-num" data-linenumber="2415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2415

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2415" class="line" lang="perl">        <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2375

</td>

<td class="new_line diff-line-num old" data-linenumber="2416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2375" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> -dbtype </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$autoblast_fileis</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -in '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -out '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2376

</td>

<td class="new_line diff-line-num old" data-linenumber="2416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2376" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> -dbtype </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$autoblast_fileis</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -in '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -out '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2377

</td>

<td class="new_line diff-line-num old" data-linenumber="2416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2377" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2416

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2416" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> -dbtype </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$autoblast_fileis</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -in '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -out '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2417

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2417" class="line" lang="perl">        <span class="nv" style="color: #008080;">$cmd</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> -dbtype </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$autoblast_fileis</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -in '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -out '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2418

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2418" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$makedb_ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="si" style="color: #d14;">$cmd</span><span class="sb" style="color: #d14;"> 3>&1 1>&2 2>&3</span><span class="p">`;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2419

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2419" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database (</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> -dbtype </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$autoblast_fileis</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -in '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -out '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'). The output is:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$makedb_ret</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2378

</td>

<td class="new_line diff-line-num" data-linenumber="2420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2420

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2420" class="line" lang="perl"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2379

</td>

<td class="new_line diff-line-num" data-linenumber="2421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2421

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2421" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">mkdir</span><span class="p">("</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB</span><span class="p">");</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2380

</td>

<td class="new_line diff-line-num" data-linenumber="2422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2422

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2422" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$keep</span><span class="p">;</span><span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>

</pre>

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

<td class="old_line diff-line-num old" data-linenumber="2381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2381

</td>

<td class="new_line diff-line-num old" data-linenumber="2423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2381" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -out '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>

</pre>

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

<td class="old_line diff-line-num new" data-linenumber="2382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2423

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2423" class="line" lang="perl">          <span class="nv" style="color: #008080;">$cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -out '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'</span><span class="p">";</span></span>

</pre>

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

<td class="old_line diff-line-num new" data-linenumber="2382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2424

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2424" class="line" lang="perl">          <span class="nv" style="color: #008080;">$makedb_ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="si" style="color: #d14;">$cmd</span><span class="sb" style="color: #d14;"> 3>&1 1>&2 2>&3</span><span class="p">`;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2425

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2425" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">ln -s '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">abs_path</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' 2>/dev/null</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2382

</td>

<td class="new_line diff-line-num" data-linenumber="2426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2426

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2426" class="line" lang="perl"></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="2383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2383

</td>

<td class="new_line diff-line-num old" data-linenumber="2427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2383" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span> <span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="p">;</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">The database generation failed once again, please <span class="idiff left">retry with 'sudo' or move the fasta files to a directory with write permissions. If this fails too, then there is</span> something wrong with the fasta files or the version of </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> cannot handle the database generation. So please try one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- update </span><span class="si" style="color: #d14;">$blastmode</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider another blast algorithm (-p)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- <span class="idiff">consider to submitting (mailing)</span> this <span class="idiff right">cas</span>e to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">incoming.gitlab.com.</span><span class="p">");}}</span></span>

</pre>

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

<td class="old_line diff-line-num new" data-linenumber="2384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2427

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2427" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span> <span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="p">;</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">The database generation failed once again, please <span class="idiff left">investigate the output from above. There is probably</span> something wrong with the fasta files or the version of </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> cannot handle the database generation. So please try one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- update </span><span class="si" style="color: #d14;">$blastmode</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider another blast algorithm (-p)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- <span class="idiff">send</span> this <span class="idiff right">issu</span>e to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">incoming.gitlab.com.</span><span class="p">");}}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2384

</td>

<td class="new_line diff-line-num" data-linenumber="2428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2428

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2428" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2385

</td>

<td class="new_line diff-line-num" data-linenumber="2429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2429

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2429" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="2386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2386

</td>

<td class="new_line diff-line-num old" data-linenumber="2430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2386" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">unlink</span><span class="p">('</span><span class="s1" style="color: #d14;">formatdb.log</span><span class="p">');</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2430

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2430" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">unlink</span><span class="p">('</span><span class="s1" style="color: #d14;">formatdb.log</span><span class="p">')</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="nv" style="color: #008080;"><span class="idiff">e</span></span><span class="idiff"> </span><span class="p"><span class="idiff">'</span></span><span class="s1" style="color: #d14;"><span class="idiff">formatdb.log</span></span><span class="p"><span class="idiff right">'</span>;</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2387

</td>

<td class="new_line diff-line-num" data-linenumber="2431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2431

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2431" class="line" lang="perl">  <span class="p">}</span><span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;"># old blastall</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2388

</td>

<td class="new_line diff-line-num" data-linenumber="2432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2432

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2432" class="line" lang="perl">    <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">@</span><span class="nv" style="color: #008080;">_</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2389

</td>

<td class="new_line diff-line-num" data-linenumber="2433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2433

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<pre style="margin: 0;"> <span id="LC2433" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 2>/dev/null</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2390

</td>

<td class="new_line diff-line-num" data-linenumber="2434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2434

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<pre style="margin: 0;"> <span id="LC2434" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2391

</td>

<td class="new_line diff-line-num" data-linenumber="2435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2435

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<pre style="margin: 0;"> <span id="LC2435" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2392

</td>

<td class="new_line diff-line-num" data-linenumber="2436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2436

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<pre style="margin: 0;"> <span id="LC2436" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2393

</td>

<td class="new_line diff-line-num old" data-linenumber="2437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2393" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -out '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2394

</td>

<td class="new_line diff-line-num old" data-linenumber="2437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2394" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -n '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2395

</td>

<td class="new_line diff-line-num old" data-linenumber="2437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2395" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2437

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2437" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -out '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2438

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2438" class="line" lang="perl">        <span class="nv" style="color: #008080;">$cmd</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -n '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'</span><span class="p">";</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="2396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2439

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2439" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$makedb_ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="si" style="color: #d14;">$cmd</span><span class="sb" style="color: #d14;"> 3>&1 1>&2 2>&3</span><span class="p">`;</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="2396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2440

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2440" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database (</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -n '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'). The output is:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$makedb_ret</span><span class="s2" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep (and use the same -project= name) for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2396

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<td class="new_line diff-line-num" data-linenumber="2441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2441

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<pre style="margin: 0;"> <span id="LC2441" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2397

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<td class="new_line diff-line-num" data-linenumber="2442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2442

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<pre style="margin: 0;"> <span id="LC2442" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">mkdir</span><span class="p">("</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2398

</td>

<td class="new_line diff-line-num" data-linenumber="2443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2443

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<pre style="margin: 0;"> <span id="LC2443" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$keep</span><span class="p">;</span><span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2399

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<td class="new_line diff-line-num old" data-linenumber="2444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2399" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -n '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2444

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2444" class="line" lang="perl">          <span class="nv" style="color: #008080;">$cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -n '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2445

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2445" class="line" lang="perl">          <span class="nv" style="color: #008080;">$makedb_ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="si" style="color: #d14;">$cmd</span><span class="sb" style="color: #d14;"> 3>&1 1>&2 2>&3</span><span class="p">`;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2446

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2446" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">ln -s '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">abs_path</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' 2>/dev/null</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2400

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<td class="new_line diff-line-num" data-linenumber="2447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2447

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2447" class="line" lang="perl"></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="2401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2401

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<td class="new_line diff-line-num old" data-linenumber="2448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2401" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span> <span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="p">;</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">The database generation failed once again, please <span class="idiff left">retry with 'sudo' or move the fasta files to a directory with write permissions. If this fails too, then there is</span> something wrong with the fasta files or the version of </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> cannot handle the database generation. So please try one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- update </span><span class="si" style="color: #d14;">$blastmode</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider another blast algorithm (-p)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- <span class="idiff">consider to submitting (mailing)</span> this <span class="idiff right">cas</span>e to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">incoming.gitlab.com.</span><span class="p">");}}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2448

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2448" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span> <span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="p">;</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">The database generation failed once again, please <span class="idiff left">investigate the output from above. There is probably</span> something wrong with the fasta files or the version of </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> cannot handle the database generation. So please try one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- update </span><span class="si" style="color: #d14;">$blastmode</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider another blast algorithm (-p)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- <span class="idiff">send</span> this <span class="idiff right">issu</span>e to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">incoming.gitlab.com.</span><span class="p">");}}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2402

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<td class="new_line diff-line-num" data-linenumber="2449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2449

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2449" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2403

</td>

<td class="new_line diff-line-num" data-linenumber="2450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2450

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2450" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="2404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2404

</td>

<td class="new_line diff-line-num old" data-linenumber="2451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2404" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">unlink</span><span class="p">('</span><span class="s1" style="color: #d14;">formatdb.log</span><span class="p">');</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2451

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2451" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">unlink</span><span class="p">('</span><span class="s1" style="color: #d14;">formatdb.log</span><span class="p">')</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="nv" style="color: #008080;"><span class="idiff">e</span></span><span class="idiff"> </span><span class="p"><span class="idiff">'</span></span><span class="s1" style="color: #d14;"><span class="idiff">formatdb.log</span></span><span class="p"><span class="idiff right">'</span>;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2405

</td>

<td class="new_line diff-line-num" data-linenumber="2452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2452

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2452" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2406

</td>

<td class="new_line diff-line-num" data-linenumber="2453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2453

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2453" class="line" lang="perl">  <span class="c1" style="color: #998; font-style: italic;">##MARK_FOR_NEW_BLAST_ALGORITHM</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2407

</td>

<td class="new_line diff-line-num" data-linenumber="2454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2454

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2454" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2431,9 +2478,7 @@ sub blast {</td>

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

<td class="old_line diff-line-num" data-linenumber="2431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2431

</td>

<td class="new_line diff-line-num" data-linenumber="2478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2478

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2478" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2432

</td>

<td class="new_line diff-line-num" data-linenumber="2479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2479

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2479" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2433

</td>

<td class="new_line diff-line-num" data-linenumber="2480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2480

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2480" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$printSTDERR</span><span class="o" style="font-weight: 600;">=</span><span class="p">"";</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="2434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2434

</td>

<td class="new_line diff-line-num old" data-linenumber="2481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2434" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">2</span><span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="2435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2435

</td>

<td class="new_line diff-line-num old" data-linenumber="2481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2435" class="line" lang="perl">    <span class="nv" style="color: #008080;">$printSTDERR</span><span class="o" style="font-weight: 600;">=</span><span class="p">'</span><span class="s1" style="color: #d14;">2>/dev/null</span><span class="p">';</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="2436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2436

</td>

<td class="new_line diff-line-num old" data-linenumber="2481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2436" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2481

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2481" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">2</span><span class="p">){</span> <span class="nv" style="color: #008080;">$printSTDERR</span><span class="o" style="font-weight: 600;">=</span><span class="p">'</span><span class="s1" style="color: #d14;">2>/dev/null</span><span class="p">';</span> <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2437

</td>

<td class="new_line diff-line-num" data-linenumber="2482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2482

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2482" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2438

</td>

<td class="new_line diff-line-num" data-linenumber="2483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2483

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2483" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$fileType</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$a</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\.(\w*)$/</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2439

</td>

<td class="new_line diff-line-num" data-linenumber="2484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2484

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2484" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2488,15 +2533,18 @@ sub blast {</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2488

</td>

<td class="new_line diff-line-num" data-linenumber="2533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2533

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2533" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$debug</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$verbose</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$command</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span>                     <span class="c1" style="color: #998; font-style: italic;"># 5.16</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2489

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<td class="new_line diff-line-num" data-linenumber="2534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2534

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2534" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2490

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<td class="new_line diff-line-num" data-linenumber="2535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2535

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<pre style="margin: 0;"> <span id="LC2535" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">diamond</span><span class="p">")</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2491

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<td class="new_line diff-line-num old" data-linenumber="2536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2491" class="line" lang="perl">      <span class="nv" style="color: #008080;">@data</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="si" style="color: #d14;">$command</span><span class="p">`;</span> <span class="c1" style="color: #998; font-style: italic;"># run diamond</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2492

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<td class="new_line diff-line-num old" data-linenumber="2536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2492" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">&Error</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed with code $?.</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The most common sources of this error are:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- no space left on device error.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- outdated </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">, please update </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> or consider another -p algorithm.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2536

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2536" class="line" lang="perl">      <span class="nv" style="color: #008080;">@data</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="si" style="color: #d14;">$command</span><span class="p">`;</span> </span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2537

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2537" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2538

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2538" class="line" lang="perl">        <span class="nv" style="color: #008080;">@data</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="si" style="color: #d14;">$command</span><span class="sb" style="color: #d14;"> --ignore-warnings</span><span class="p">`;</span></span>

</pre>

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

<td class="old_line diff-line-num new" data-linenumber="2493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2539

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2539" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed with code $?</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (</span><span class="si" style="color: #d14;">$command</span><span class="s2" style="color: #d14;">). (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The most common sources of this error are:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- no space left on device error.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- outdated </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">, please update </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> or consider another -p algorithm.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.</span><span class="p">")</span> <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2540

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2540" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2493

</td>

<td class="new_line diff-line-num" data-linenumber="2541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2541

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2541" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">test_sort</span><span class="p">"){</span><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="p">"</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp</span><span class="p">"</span><span class="o" style="font-weight: 600;">></span><span class="p">){</span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/[^\t]+([,])[^\t]+[eE]/</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="s2" style="color: #d14;">found forbidden symbol '$1' at </span><span class="si" style="color: #d14;">$_</span><span class="s2" style="color: #d14;"> in </span><span class="si" style="color: #d14;">$bla</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">&reset_locale</span><span class="p">();</span><span class="nb" style="color: #0086b3;">die</span><span class="p">;}}}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2494

</td>

<td class="new_line diff-line-num" data-linenumber="2542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2542

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2542" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$keep</span><span class="p">){</span><span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">mv '</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp' '</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">'</span><span class="p">");}</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2495

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<td class="new_line diff-line-num" data-linenumber="2543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2543

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2543" class="line" lang="perl"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2496

</td>

<td class="new_line diff-line-num" data-linenumber="2544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2544

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2544" class="line" lang="perl">    <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">rapsearch</span><span class="p">")</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2497

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<td class="new_line diff-line-num" data-linenumber="2545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2545

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<pre style="margin: 0;"> <span id="LC2545" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2498

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<td class="new_line diff-line-num" data-linenumber="2546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2546

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<pre style="margin: 0;"> <span id="LC2546" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$command</span><span class="p">");</span></span>

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<td class="old_line diff-line-num old" data-linenumber="2499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2499

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<td class="new_line diff-line-num old" data-linenumber="2547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2499" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">&Error</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed with code $?<span class="idiff left right">.</span></span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The most common sources of this error are:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- no space left on device error.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- outdated </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">, please update </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> or consider another -p algorithm.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.</span><span class="p">");}</span></span>

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<td class="old_line diff-line-num new" data-linenumber="2500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2547

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<pre style="margin: 0;">+<span id="LC2547" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">&Error</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed with code $?</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> <span class="idiff left">(</span></span><span class="si" style="color: #d14;"><span class="idiff">$command</span></span><span class="s2" style="color: #d14;"><span class="idiff right">). </span>(Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The most common sources of this error are:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- no space left on device error.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- outdated </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">, please update </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> or consider another -p algorithm.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.</span><span class="p">");}</span></span>

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<td class="old_line diff-line-num" data-linenumber="2500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2500

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<td class="new_line diff-line-num" data-linenumber="2548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2548

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<pre style="margin: 0;"> <span id="LC2548" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;"># NOTE -s f does not work everytime, therefore here is a conversion of -s t to f (ln -> evalues)</span></span>

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<td class="old_line diff-line-num" data-linenumber="2501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2501

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<td class="new_line diff-line-num" data-linenumber="2549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2549

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<pre style="margin: 0;"> <span id="LC2549" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: #008080;">OUTM</span><span class="p">,"</span><span class="s2" style="color: #d14;">>></span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.m82</span><span class="p">");</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: #008080;">INM</span><span class="p">,"</span><span class="s2" style="color: #d14;"><</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp.m8</span><span class="p">");</span></span>

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<td class="old_line diff-line-num" data-linenumber="2502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2502

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<td class="new_line diff-line-num" data-linenumber="2550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2550

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<pre style="margin: 0;"> <span id="LC2550" class="line" lang="perl">      <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: #008080;">INM</span><span class="o" style="font-weight: 600;">></span><span class="p">){</span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="vg" style="color: #008080;">$_</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="vg" style="color: #008080;">$_</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="ow" style="font-weight: 600;">eq</span><span class="p">"</span><span class="s2" style="color: #d14;">#</span><span class="p">"){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@arr</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\t</span><span class="p">",</span><span class="vg" style="color: #008080;">$_</span><span class="p">);</span> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">OUTM</span> <span class="nv" style="color: #008080;">$arr</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="p">"</span><span class="se" style="color: #d14;">\t</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$arr</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\t</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$arr</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\t</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$arr</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\t</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$arr</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\t</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$arr</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\t</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$arr</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\t</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$arr</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\t</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$arr</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\t</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$arr</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\t</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exp</span><span class="p">(</span><span class="nv" style="color: #008080;">$arr</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">])</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\t</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$arr</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">];}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2510,7 +2558,7 @@ sub blast {</td>

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<td class="old_line diff-line-num" data-linenumber="2510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="2558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2558" class="line" lang="perl">    <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">usearch</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">ublast</span><span class="p">")</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="2511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2511

</td>

<td class="new_line diff-line-num" data-linenumber="2559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2559

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2559" class="line" lang="perl"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2512

</td>

<td class="new_line diff-line-num" data-linenumber="2560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2560

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2560" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$command</span><span class="p">");</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="2513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2513

</td>

<td class="new_line diff-line-num old" data-linenumber="2561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2513" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">&Error</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed with code $?<span class="idiff left right">.</span></span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The most common sources of this error are:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- no space left on device error.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- outdated </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">, please update </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> or consider another -p algorithm.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2561

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2561" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">&Error</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed with code $?</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> <span class="idiff left">(</span></span><span class="si" style="color: #d14;"><span class="idiff">$command</span></span><span class="s2" style="color: #d14;"><span class="idiff right">). </span>(Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The most common sources of this error are:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- no space left on device error.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- outdated </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">, please update </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> or consider another -p algorithm.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2514

</td>

<td class="new_line diff-line-num" data-linenumber="2562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2562

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2562" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">test_sort</span><span class="p">"){</span><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="p">"</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp</span><span class="p">"</span><span class="o" style="font-weight: 600;">></span><span class="p">){</span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/[^\t]+([,])[^\t]+[eE]/</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="s2" style="color: #d14;">found forbidden symbol '$1' at </span><span class="si" style="color: #d14;">$_</span><span class="s2" style="color: #d14;"> in </span><span class="si" style="color: #d14;">$bla</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">&reset_locale</span><span class="p">();</span><span class="nb" style="color: #0086b3;">die</span><span class="p">;}}}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2515

</td>

<td class="new_line diff-line-num" data-linenumber="2563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2563

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2563" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">perl </span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_formatUsearch.pl '</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp' >'</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">'</span><span class="p">");</span> <span class="c1" style="color: #998; font-style: italic;"># problem with ublast/usearch: gene names include the description.</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2516

</td>

<td class="new_line diff-line-num" data-linenumber="2564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2564

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2564" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">unlink</span> <span class="p">"</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp</span><span class="p">";</span></span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2518,7 +2566,7 @@ sub blast {</td>

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<td class="old_line diff-line-num" data-linenumber="2518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2518

</td>

<td class="new_line diff-line-num" data-linenumber="2566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2566

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2566" class="line" lang="perl">    <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">topaz</span><span class="p">")</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2519

</td>

<td class="new_line diff-line-num" data-linenumber="2567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2567

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2567" class="line" lang="perl"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2520

</td>

<td class="new_line diff-line-num" data-linenumber="2568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2568

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2568" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$command</span><span class="p">");</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="2521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2521

</td>

<td class="new_line diff-line-num old" data-linenumber="2569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2521" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">&Error</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed with code $?<span class="idiff left right">.</span></span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The most common sources of this error are:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- no space left on device error.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- outdated </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">, please update </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> or consider another -p algorithm.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.</span><span class="p">");}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2569

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<pre style="margin: 0;">+<span id="LC2569" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">&Error</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed with code $?</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> <span class="idiff left">(</span></span><span class="si" style="color: #d14;"><span class="idiff">$command</span></span><span class="s2" style="color: #d14;"><span class="idiff right">). </span>(Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The most common sources of this error are:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- no space left on device error.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- outdated </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">, please update </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> or consider another -p algorithm.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2522

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<td class="new_line diff-line-num" data-linenumber="2570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2570

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<pre style="margin: 0;"> <span id="LC2570" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">test_sort</span><span class="p">"){</span><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="p">"</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp</span><span class="p">"</span><span class="o" style="font-weight: 600;">></span><span class="p">){</span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/[^\t]+([,])[^\t]+[eE]/</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="s2" style="color: #d14;">found forbidden symbol '$1' at </span><span class="si" style="color: #d14;">$_</span><span class="s2" style="color: #d14;"> in </span><span class="si" style="color: #d14;">$bla</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">&reset_locale</span><span class="p">();</span><span class="nb" style="color: #0086b3;">die</span><span class="p">;}}}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2523

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<td class="new_line diff-line-num" data-linenumber="2571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2571

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<pre style="margin: 0;"> <span id="LC2571" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">tail -n +2 '</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp' > '</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">'</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2524

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<td class="new_line diff-line-num" data-linenumber="2572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2572

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<pre style="margin: 0;"> <span id="LC2572" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">unlink</span> <span class="p">"</span><span class="s2" style="color: #d14;">timing.txt</span><span class="p">";</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2527,14 +2575,14 @@ sub blast {</td>

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<td class="old_line diff-line-num" data-linenumber="2527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2527

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<td class="new_line diff-line-num" data-linenumber="2575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2575

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<pre style="margin: 0;"> <span id="LC2575" class="line" lang="perl">    <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">lastp</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">lastn</span><span class="p">")</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2528

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<td class="new_line diff-line-num" data-linenumber="2576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2576

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2576" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2529

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<td class="new_line diff-line-num" data-linenumber="2577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2577

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<pre style="margin: 0;"> <span id="LC2577" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$command</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2530

</td>

<td class="new_line diff-line-num old" data-linenumber="2578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2530" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">&Error</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed with code $?<span class="idiff left right">.</span></span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The most common sources of this error are:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- no space left on device error.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- outdated </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">, please update </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> or consider another -p algorithm.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2578

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2578" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">&Error</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed with code $?</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> <span class="idiff left">(</span></span><span class="si" style="color: #d14;"><span class="idiff">$command</span></span><span class="s2" style="color: #d14;"><span class="idiff right">). </span>(Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The most common sources of this error are:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- no space left on device error.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- outdated </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">, please update </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> or consider another -p algorithm.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2531

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<td class="new_line diff-line-num" data-linenumber="2579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2579

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2579" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">test_sort</span><span class="p">"){</span><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="p">"</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp</span><span class="p">"</span><span class="o" style="font-weight: 600;">></span><span class="p">){</span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/[^\t]+([,])[^\t]+[eE]/</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="s2" style="color: #d14;">found forbidden symbol '$1' at </span><span class="si" style="color: #d14;">$_</span><span class="s2" style="color: #d14;"> in </span><span class="si" style="color: #d14;">$bla</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">&reset_locale</span><span class="p">();</span><span class="nb" style="color: #0086b3;">die</span><span class="p">;}}}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2532

</td>

<td class="new_line diff-line-num" data-linenumber="2580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2580

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2580" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">mv '</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp' '</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">'</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2533

</td>

<td class="new_line diff-line-num" data-linenumber="2581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2581

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2581" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2534

</td>

<td class="new_line diff-line-num" data-linenumber="2582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2582

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2582" class="line" lang="perl">    <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/.*blat.*/</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2535

</td>

<td class="new_line diff-line-num" data-linenumber="2583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2583

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2583" class="line" lang="perl"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2536

</td>

<td class="new_line diff-line-num" data-linenumber="2584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2584

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2584" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$command</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2537

</td>

<td class="new_line diff-line-num old" data-linenumber="2585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2537" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">&Error</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed with code $?<span class="idiff left right">.</span></span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The most common sources of this error are:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- no space left on device error.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- outdated </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">, please update </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> or consider another -p algorithm.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.</span><span class="p">");}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2585

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2585" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">&Error</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed with code $?</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> <span class="idiff left">(</span></span><span class="si" style="color: #d14;"><span class="idiff">$command</span></span><span class="s2" style="color: #d14;"><span class="idiff right">). </span>(Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The most common sources of this error are:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- no space left on device error.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- outdated </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">, please update </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> or consider another -p algorithm.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2538

</td>

<td class="new_line diff-line-num" data-linenumber="2586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2586

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2586" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">test_sort</span><span class="p">"){</span><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="p">"</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp</span><span class="p">"</span><span class="o" style="font-weight: 600;">></span><span class="p">){</span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/[^\t]+([,])[^\t]+[eE]/</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="s2" style="color: #d14;">found forbidden symbol '$1' at </span><span class="si" style="color: #d14;">$_</span><span class="s2" style="color: #d14;"> in </span><span class="si" style="color: #d14;">$bla</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">&reset_locale</span><span class="p">();</span><span class="nb" style="color: #0086b3;">die</span><span class="p">;}}}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2539

</td>

<td class="new_line diff-line-num" data-linenumber="2587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2587

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2587" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">('</span><span class="s1" style="color: #d14;">awk -F</span><span class="se" style="color: #d14;">\'</span><span class="s1" style="color: #d14;">\t</span><span class="se" style="color: #d14;">\'</span><span class="s1" style="color: #d14;"> </span><span class="se" style="color: #d14;">\'</span><span class="s1" style="color: #d14;">{if($11<</span><span class="p">'</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$evalue</span><span class="o" style="font-weight: 600;">.</span><span class="p">'</span><span class="s1" style="color: #d14;">)print $0}</span><span class="se" style="color: #d14;">\'</span><span class="s1" style="color: #d14;"> </span><span class="se" style="color: #d14;">\'</span><span class="p">'</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$bla</span><span class="o" style="font-weight: 600;">.</span><span class="p">'</span><span class="s1" style="color: #d14;">.tmp</span><span class="se" style="color: #d14;">\'</span><span class="s1" style="color: #d14;"> > </span><span class="se" style="color: #d14;">\'</span><span class="p">'</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$bla</span><span class="o" style="font-weight: 600;">.</span><span class="p">'</span><span class="se" style="color: #d14;">\'</span><span class="p">');</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2540

</td>

<td class="new_line diff-line-num" data-linenumber="2588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2588

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2588" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">unlink</span> <span class="p">"</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp</span><span class="p">";</span></span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2542,7 +2590,7 @@ sub blast {</td>

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<td class="old_line diff-line-num" data-linenumber="2542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2542

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<td class="new_line diff-line-num" data-linenumber="2590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2590

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<pre style="margin: 0;"> <span id="LC2590" class="line" lang="perl">    <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">mmseqsn</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">mmseqsp</span><span class="p">")</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2543

</td>

<td class="new_line diff-line-num" data-linenumber="2591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2591

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2591" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2544

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<td class="new_line diff-line-num" data-linenumber="2592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2592

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<pre style="margin: 0;"> <span id="LC2592" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$command</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2545

</td>

<td class="new_line diff-line-num old" data-linenumber="2593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2545" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">&Error</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed with code $?<span class="idiff left right">.</span></span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The most common sources of this error are:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- no space left on device error.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- outdated </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">, please update </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> or consider another -p algorithm.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2593

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<pre style="margin: 0;">+<span id="LC2593" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">&Error</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed with code $?</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> <span class="idiff left">(</span></span><span class="si" style="color: #d14;"><span class="idiff">$command</span></span><span class="s2" style="color: #d14;"><span class="idiff right">). </span>(Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The most common sources of this error are:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- no space left on device error.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- outdated </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">, please update </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> or consider another -p algorithm.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2546

</td>

<td class="new_line diff-line-num" data-linenumber="2594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2594

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2594" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">(</span><span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">mmseqs convertalis '</span><span class="si" style="color: #d14;">$b</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$a</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp' '</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp2' ></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null 2></span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2547

</td>

<td class="new_line diff-line-num" data-linenumber="2595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2595

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2595" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2548

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<td class="new_line diff-line-num" data-linenumber="2596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2596

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2596" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">test_sort</span><span class="p">"){</span><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="p">"</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp</span><span class="p">"</span><span class="o" style="font-weight: 600;">></span><span class="p">){</span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/[^\t]+([,])[^\t]+[eE]/</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="s2" style="color: #d14;">found forbidden symbol '$1' at </span><span class="si" style="color: #d14;">$_</span><span class="s2" style="color: #d14;"> in </span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">&reset_locale</span><span class="p">();</span><span class="nb" style="color: #0086b3;">die</span><span class="p">;}}}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2556,7 +2604,7 @@ sub blast {</td>

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<td class="old_line diff-line-num" data-linenumber="2556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2556

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<td class="new_line diff-line-num" data-linenumber="2604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2604

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<pre style="margin: 0;"> <span id="LC2604" class="line" lang="perl">    <span class="p">}</span><span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;"># -p=blastp,blastn,autoblast, ...</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2557

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<td class="new_line diff-line-num" data-linenumber="2605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2605

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2605" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2558

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<td class="new_line diff-line-num" data-linenumber="2606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2606

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<pre style="margin: 0;"> <span id="LC2606" class="line" lang="perl">      <span class="nv" style="color: #008080;">@data</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="si" style="color: #d14;">$command</span><span class="p">`;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2559

</td>

<td class="new_line diff-line-num old" data-linenumber="2607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2559" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">&Error</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed with code $?<span class="idiff left right">.</span></span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The most common sources of this error are:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- no space left on device error.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- outdated </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">, please update </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> or consider another -p algorithm.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2607

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<pre style="margin: 0;">+<span id="LC2607" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">&Error</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed with code $?</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> <span class="idiff left">(</span></span><span class="si" style="color: #d14;"><span class="idiff">$command</span></span><span class="s2" style="color: #d14;"><span class="idiff right">). </span>(Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The most common sources of this error are:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- no space left on device error.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- outdated </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">, please update </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> or consider another -p algorithm.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2560

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<td class="new_line diff-line-num" data-linenumber="2608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2608

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<pre style="margin: 0;"> <span id="LC2608" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">test_sort</span><span class="p">"){</span><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="p">"</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp</span><span class="p">"</span><span class="o" style="font-weight: 600;">></span><span class="p">){</span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/[^\t]+([,])[^\t]+[eE]/</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="s2" style="color: #d14;">found forbidden symbol '$1' at </span><span class="si" style="color: #d14;">$_</span><span class="s2" style="color: #d14;"> in </span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">&reset_locale</span><span class="p">();</span><span class="nb" style="color: #0086b3;">die</span><span class="p">;}}}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2561

</td>

<td class="new_line diff-line-num" data-linenumber="2609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2609

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<pre style="margin: 0;"> <span id="LC2609" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$keep</span><span class="p">){</span><span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">mv '</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp' '</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">'</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2562

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<td class="new_line diff-line-num" data-linenumber="2610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2610

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<pre style="margin: 0;"> <span id="LC2610" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2614,8 +2662,8 @@ sub check_bins {</td>

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<td class="old_line diff-line-num" data-linenumber="2614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2614

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<td class="new_line diff-line-num" data-linenumber="2662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2662

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<pre style="margin: 0;"> <span id="LC2662" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@version</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\s+/</span><span class="p">,</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2615

</td>

<td class="new_line diff-line-num" data-linenumber="2663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2663

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<pre style="margin: 0;"> <span id="LC2663" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$versionnumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">pop</span> <span class="nv" style="color: #008080;">@version</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2616

</td>

<td class="new_line diff-line-num" data-linenumber="2664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2664

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<pre style="margin: 0;"> <span id="LC2664" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;"># Commands</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2617

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<td class="new_line diff-line-num old" data-linenumber="2665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2617" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span>  <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">blastp+</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">makeblastdb -dbtype prot -in</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2618

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<td class="new_line diff-line-num old" data-linenumber="2665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2618" class="line" lang="perl">      <span class="k" style="font-weight: 600;">elsif</span> <span class="idiff left right">  </span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">blastn+</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">tblastx+</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">makeblastdb -dbtype nucl -in</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2665

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<pre style="margin: 0;">+<span id="LC2665" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span>  <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">blastp+</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">makeblastdb </span><span class="si" style="color: #d14;"><span class="idiff left">$makeBlastOptions</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> </span>-dbtype prot -in</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2666

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<pre style="margin: 0;">+<span id="LC2666" class="line" lang="perl">      <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">blastn+</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">tblastx+</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">makeblastdb </span><span class="si" style="color: #d14;"><span class="idiff left">$makeBlastOptions</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> </span>-dbtype nucl -in</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2619

</td>

<td class="new_line diff-line-num" data-linenumber="2667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2667

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<pre style="margin: 0;"> <span id="LC2667" class="line" lang="perl">      <span class="k" style="font-weight: 600;">else</span>  <span class="p">{</span><span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">This should not happen! Please submit the FASTA file(s) and the parameter vector (above) to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">incoming.gitlab.com to help fixing this issue.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2620

</td>

<td class="new_line diff-line-num" data-linenumber="2668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2668

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2668" class="line" lang="perl"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2621

</td>

<td class="new_line diff-line-num" data-linenumber="2669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2669

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<pre style="margin: 0;"> <span id="LC2669" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Detected '</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' version </span><span class="si" style="color: #d14;">$versionnumber</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$blastversion</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$versionnumber</span><span class="p">;}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2634,7 +2682,7 @@ sub check_bins {</td>

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<td class="old_line diff-line-num" data-linenumber="2634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2634

</td>

<td class="new_line diff-line-num" data-linenumber="2682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2682

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<pre style="margin: 0;"> <span id="LC2682" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@version</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\s+/</span><span class="p">,</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2635

</td>

<td class="new_line diff-line-num" data-linenumber="2683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2683

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<pre style="margin: 0;"> <span id="LC2683" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$versionnumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">pop</span> <span class="nv" style="color: #008080;">@version</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2636

</td>

<td class="new_line diff-line-num" data-linenumber="2684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2684

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<pre style="margin: 0;"> <span id="LC2684" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;"># Commands</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="2637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2637

</td>

<td class="new_line diff-line-num old" data-linenumber="2685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2637" class="line" lang="perl">      <span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">makeblastdb </span><span class="p">";</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2685

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2685" class="line" lang="perl">      <span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">makeblastdb </span><span class="si" style="color: #d14;"><span class="idiff left">$makeBlastOptions</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> </span></span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2638

</td>

<td class="new_line diff-line-num" data-linenumber="2686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2686

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2686" class="line" lang="perl">      </span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2639

</td>

<td class="new_line diff-line-num" data-linenumber="2687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2687

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<pre style="margin: 0;"> <span id="LC2687" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Detected 'blast+' version </span><span class="si" style="color: #d14;">$versionnumber</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$blastversion</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$versionnumber</span><span class="p">;}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2640

</td>

<td class="new_line diff-line-num" data-linenumber="2688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2688

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<pre style="margin: 0;"> <span id="LC2688" class="line" lang="perl">      <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2650,9 +2698,9 @@ sub check_bins {</td>

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<td class="old_line diff-line-num" data-linenumber="2650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2650

</td>

<td class="new_line diff-line-num" data-linenumber="2698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2698

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<pre style="margin: 0;"> <span id="LC2698" class="line" lang="perl">      <span class="vg" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[\r\n]+$//</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2651

</td>

<td class="new_line diff-line-num" data-linenumber="2699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2699

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<pre style="margin: 0;"> <span id="LC2699" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/blastall.+?([^\s]+)/</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2652

</td>

<td class="new_line diff-line-num" data-linenumber="2700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2700

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<pre style="margin: 0;"> <span id="LC2700" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$versionnumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="2653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2653

</td>

<td class="new_line diff-line-num old" data-linenumber="2701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC2653" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span>  <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">blastp_legacy</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">formatdb -p T -o F -i</span><span class="p">";}</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="2654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2654

</td>

<td class="new_line diff-line-num old" data-linenumber="2701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC2654" class="line" lang="perl">        <span class="k" style="font-weight: 600;">elsif</span>   <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">blastn</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">formatdb -p F -o F -i</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2655

</td>

<td class="new_line diff-line-num old" data-linenumber="2701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2655" class="line" lang="perl">        <span class="k" style="font-weight: 600;">elsif</span>   <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">tblastx</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">formatdb -p F -o F -i</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2701

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<pre style="margin: 0;">+<span id="LC2701" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span>  <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">blastp_legacy</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">formatdb </span><span class="si" style="color: #d14;"><span class="idiff left">$makeBlastOptions</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> </span>-p T -o F -i</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2702

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<pre style="margin: 0;">+<span id="LC2702" class="line" lang="perl">        <span class="k" style="font-weight: 600;">elsif</span>   <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">blastn</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">formatdb </span><span class="si" style="color: #d14;"><span class="idiff left">$makeBlastOptions</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> </span>-p F -o F -i</span><span class="p">";}</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="2656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2703

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<pre style="margin: 0;">+<span id="LC2703" class="line" lang="perl">        <span class="k" style="font-weight: 600;">elsif</span>   <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">tblastx</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">formatdb </span><span class="si" style="color: #d14;"><span class="idiff left">$makeBlastOptions</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> </span>-p F -o F -i</span><span class="p">";}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2656

</td>

<td class="new_line diff-line-num" data-linenumber="2704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2704

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2704" class="line" lang="perl">        <span class="k" style="font-weight: 600;">else</span>  <span class="p">{</span><span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">This should not happen! Please submit the FASTA file(s) and the parameter vector (above to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">incoming.gitlab.com to help fixing this issue.</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2657

</td>

<td class="new_line diff-line-num" data-linenumber="2705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2705

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2705" class="line" lang="perl"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2658

</td>

<td class="new_line diff-line-num" data-linenumber="2706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2706

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2706" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Detected '</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' version </span><span class="si" style="color: #d14;">$versionnumber</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$blastversion</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$versionnumber</span><span class="p">;}</span></span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2669,7 +2717,7 @@ sub check_bins {</td>

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<td class="old_line diff-line-num" data-linenumber="2669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2669

</td>

<td class="new_line diff-line-num" data-linenumber="2717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2717

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2717" class="line" lang="perl">    <span class="k" style="font-weight: 600;">foreach</span> <span class="p">(</span><span class="nv" style="color: #008080;">@topazv</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2670

</td>

<td class="new_line diff-line-num" data-linenumber="2718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2718

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2718" class="line" lang="perl">      <span class="vg" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[\r\n]+$//</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2671

</td>

<td class="new_line diff-line-num" data-linenumber="2719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2719

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2719" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/usage: TOPAZ(.+)/</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="2672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2672

</td>

<td class="new_line diff-line-num old" data-linenumber="2720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2672" class="line" lang="perl">        <span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">topaz</span><span class="p">";</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="2673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2720

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2720" class="line" lang="perl">        <span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">topaz<span class="idiff left"> </span></span><span class="si" style="color: #d14;"><span class="idiff right">$makeBlastOptions</span></span><span class="p">";</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2673

</td>

<td class="new_line diff-line-num" data-linenumber="2721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2721

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2721" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Detected '</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2674

</td>

<td class="new_line diff-line-num" data-linenumber="2722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2722

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2722" class="line" lang="perl">        <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2675

</td>

<td class="new_line diff-line-num" data-linenumber="2723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2723

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2723" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2719,7 +2767,7 @@ sub check_bins {</td>

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<td class="old_line diff-line-num" data-linenumber="2719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2719

</td>

<td class="new_line diff-line-num" data-linenumber="2767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2767

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2767" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$out</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$out</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/rapsearch\sv([\d\.]*)/</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2720

</td>

<td class="new_line diff-line-num" data-linenumber="2768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2768

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2768" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@version</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\s+/</span><span class="p">,</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</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="2721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2721

</td>

<td class="new_line diff-line-num" data-linenumber="2769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2769

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<pre style="margin: 0;"> <span id="LC2769" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$versionnumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">pop</span> <span class="nv" style="color: #008080;">@version</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="2722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2722

</td>

<td class="new_line diff-line-num old" data-linenumber="2770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2722" class="line" lang="perl">      <span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">prerapsearch</span><span class="p">";</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2770

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2770" class="line" lang="perl">      <span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">prerapsearch<span class="idiff left"> </span></span><span class="si" style="color: #d14;"><span class="idiff right">$makeBlastOptions</span></span><span class="p">";</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2723

</td>

<td class="new_line diff-line-num" data-linenumber="2771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2771

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2771" class="line" lang="perl">     <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Detected '</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' version </span><span class="si" style="color: #d14;">$versionnumber</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$blastversion</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$versionnumber</span><span class="p">;}</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2724

</td>

<td class="new_line diff-line-num" data-linenumber="2772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2772

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2772" class="line" lang="perl">      <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2725

</td>

<td class="new_line diff-line-num" data-linenumber="2773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2773

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2773" class="line" lang="perl">    <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2738,7 +2786,7 @@ sub check_bins {</td>

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<td class="old_line diff-line-num" data-linenumber="2738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2738

</td>

<td class="new_line diff-line-num" data-linenumber="2786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2786

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2786" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$out</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$out</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/([a-zA-Z0-9]+)/</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2739

</td>

<td class="new_line diff-line-num" data-linenumber="2787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2787

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2787" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@version</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\s+/</span><span class="p">,</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</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="2740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2740

</td>

<td class="new_line diff-line-num" data-linenumber="2788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2788

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<pre style="margin: 0;"> <span id="LC2788" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$versionnumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">pop</span> <span class="nv" style="color: #008080;">@version</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2741

</td>

<td class="new_line diff-line-num old" data-linenumber="2789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2741" class="line" lang="perl">      <span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">mmseqs createdb</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2789

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<pre style="margin: 0;">+<span id="LC2789" class="line" lang="perl">      <span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">mmseqs createdb<span class="idiff left"> </span></span><span class="si" style="color: #d14;"><span class="idiff right">$makeBlastOptions</span></span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2742

</td>

<td class="new_line diff-line-num" data-linenumber="2790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2790

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<pre style="margin: 0;"> <span id="LC2790" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Detected '</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' version </span><span class="si" style="color: #d14;">$versionnumber</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$blastversion</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$versionnumber</span><span class="p">;}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2743

</td>

<td class="new_line diff-line-num" data-linenumber="2791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2791

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<pre style="margin: 0;"> <span id="LC2791" class="line" lang="perl">      <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2744

</td>

<td class="new_line diff-line-num" data-linenumber="2792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2792

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<pre style="margin: 0;"> <span id="LC2792" class="line" lang="perl">    <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2759,7 +2807,7 @@ sub check_bins {</td>

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<td class="old_line diff-line-num" data-linenumber="2759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2759

</td>

<td class="new_line diff-line-num" data-linenumber="2807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2807

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<pre style="margin: 0;"> <span id="LC2807" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$out</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$out</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/diamond\sversion\s(.+)\n/</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2760

</td>

<td class="new_line diff-line-num" data-linenumber="2808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2808

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<pre style="margin: 0;"> <span id="LC2808" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@version</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\s+/</span><span class="p">,</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2761

</td>

<td class="new_line diff-line-num" data-linenumber="2809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2809

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<pre style="margin: 0;"> <span id="LC2809" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$versionnumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">pop</span> <span class="nv" style="color: #008080;">@version</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2762

</td>

<td class="new_line diff-line-num old" data-linenumber="2810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2762" class="line" lang="perl">      <span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">diamond makedb --in</span><span class="p">";</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2810

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2810" class="line" lang="perl">      <span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">diamond makedb </span><span class="si" style="color: #d14;"><span class="idiff left">$makeBlastOptions</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> </span>--in</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2763

</td>

<td class="new_line diff-line-num" data-linenumber="2811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2811

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2811" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Detected '</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' version </span><span class="si" style="color: #d14;">$versionnumber</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$blastversion</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$versionnumber</span><span class="p">;}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2764

</td>

<td class="new_line diff-line-num" data-linenumber="2812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2812

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2812" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$versionnumber</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^0\.9\.(\d+)/</span><span class="p">){</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">29</span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2765

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<td class="new_line diff-line-num" data-linenumber="2813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2813

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2813" class="line" lang="perl">        <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">!!!! </span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">WARNING '</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' version </span><span class="si" style="color: #d14;">$versionnumber</span><span class="s2" style="color: #d14;"> has a known bug that incorrectly computes the length of an alignment, thus the coverage threshold can produce wrong results leading in false negatives. See https://gitlab.com/paulklemm_PHD/proteinortho/issues/24 for more details.</span><span class="se" style="color: #d14;">\n\n</span><span class="s2" style="color: #d14;"> >>> Please update diamond to 0.9.29 or higher <<<</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2783,7 +2831,7 @@ sub check_bins {</td>

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<td class="old_line diff-line-num" data-linenumber="2783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2783

</td>

<td class="new_line diff-line-num" data-linenumber="2831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2831

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<pre style="margin: 0;"> <span id="LC2831" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$out</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$out</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/usearch\sv(.+)\n/</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2784

</td>

<td class="new_line diff-line-num" data-linenumber="2832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2832

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<pre style="margin: 0;"> <span id="LC2832" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@version</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\s+/</span><span class="p">,</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2785

</td>

<td class="new_line diff-line-num" data-linenumber="2833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2833

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<pre style="margin: 0;"> <span id="LC2833" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$versionnumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">pop</span> <span class="nv" style="color: #008080;">@version</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2786

</td>

<td class="new_line diff-line-num old" data-linenumber="2834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2786" class="line" lang="perl">      <span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">usearch -makeudb_ublast</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2834

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<pre style="margin: 0;">+<span id="LC2834" class="line" lang="perl">      <span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">usearch </span><span class="si" style="color: #d14;"><span class="idiff left">$makeBlastOptions</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> </span>-makeudb_ublast</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2787

</td>

<td class="new_line diff-line-num" data-linenumber="2835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2835

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<pre style="margin: 0;"> <span id="LC2835" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Detected '</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' version </span><span class="si" style="color: #d14;">$versionnumber</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$blastversion</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$versionnumber</span><span class="p">;}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2788

</td>

<td class="new_line diff-line-num" data-linenumber="2836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2836

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<pre style="margin: 0;"> <span id="LC2836" class="line" lang="perl">      <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2789

</td>

<td class="new_line diff-line-num" data-linenumber="2837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2837

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<pre style="margin: 0;"> <span id="LC2837" class="line" lang="perl">    <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2802,7 +2850,7 @@ sub check_bins {</td>

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<td class="old_line diff-line-num" data-linenumber="2802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2802

</td>

<td class="new_line diff-line-num" data-linenumber="2850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2850

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<pre style="margin: 0;"> <span id="LC2850" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$out</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$out</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/usearch\sv(.+)\n/</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2803

</td>

<td class="new_line diff-line-num" data-linenumber="2851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2851

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<pre style="margin: 0;"> <span id="LC2851" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@version</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\s+/</span><span class="p">,</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2804

</td>

<td class="new_line diff-line-num" data-linenumber="2852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2852

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2852" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$versionnumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">pop</span> <span class="nv" style="color: #008080;">@version</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="2805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2805

</td>

<td class="new_line diff-line-num old" data-linenumber="2853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2805" class="line" lang="perl">      <span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">usearch -makeudb_usearch</span><span class="p">";</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2853

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2853" class="line" lang="perl">      <span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">usearch </span><span class="si" style="color: #d14;"><span class="idiff left">$makeBlastOptions</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> </span>-makeudb_usearch</span><span class="p">";</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2806

</td>

<td class="new_line diff-line-num" data-linenumber="2854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2854

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2854" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Detected '</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' version </span><span class="si" style="color: #d14;">$versionnumber</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$blastversion</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$versionnumber</span><span class="p">;}</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2807

</td>

<td class="new_line diff-line-num" data-linenumber="2855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2855

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2855" class="line" lang="perl">      <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2808

</td>

<td class="new_line diff-line-num" data-linenumber="2856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2856

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2856" class="line" lang="perl">    <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2821,7 +2869,7 @@ sub check_bins {</td>

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<td class="old_line diff-line-num" data-linenumber="2821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2821

</td>

<td class="new_line diff-line-num" data-linenumber="2869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2869

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2869" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$out</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$out</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/lastal\s(.+)\n/</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2822

</td>

<td class="new_line diff-line-num" data-linenumber="2870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2870

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2870" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@version</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\s+/</span><span class="p">,</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2823

</td>

<td class="new_line diff-line-num" data-linenumber="2871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2871

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2871" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$versionnumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">pop</span> <span class="nv" style="color: #008080;">@version</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="2824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2824

</td>

<td class="new_line diff-line-num old" data-linenumber="2872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2824" class="line" lang="perl">      <span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">lastdb</span><span class="p">";</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2872

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2872" class="line" lang="perl">      <span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">lastdb<span class="idiff left"> </span></span><span class="si" style="color: #d14;"><span class="idiff right">$makeBlastOptions</span></span><span class="p">";</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2825

</td>

<td class="new_line diff-line-num" data-linenumber="2873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2873

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2873" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Detected '</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' version </span><span class="si" style="color: #d14;">$versionnumber</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$blastversion</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$versionnumber</span><span class="p">;}</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2826

</td>

<td class="new_line diff-line-num" data-linenumber="2874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2874

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2874" class="line" lang="perl">      <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2827

</td>

<td class="new_line diff-line-num" data-linenumber="2875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2875

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2875" class="line" lang="perl">    <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2843,15 +2891,25 @@ sub check_bins {</td>

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<td class="old_line diff-line-num" data-linenumber="2843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2843

</td>

<td class="new_line diff-line-num" data-linenumber="2891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2891

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2891" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2844

</td>

<td class="new_line diff-line-num" data-linenumber="2892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2892

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2892" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Check plausibility of files</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2845

</td>

<td class="new_line diff-line-num" data-linenumber="2893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2893

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2893" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">check_files</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2894

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2894" class="line" lang="perl">  <span class="nv" style="color: #008080;">RESTART_check_files:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2895

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2895" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2846

</td>

<td class="new_line diff-line-num" data-linenumber="2896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2896

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2896" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="p">(</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$selfblast</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$step</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="nv" style="color: #008080;">&print_usage</span><span class="p">;</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">I need at least two files to compare something!</span><span class="p">");}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2847

</td>

<td class="new_line diff-line-num" data-linenumber="2897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2897

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2897" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Checking input files</span><span class="p">";</span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$checkfasta</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;"> carefully (-checkfasta).</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="p">";}}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2848

</td>

<td class="new_line diff-line-num" data-linenumber="2898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2898

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2898" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2899

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2899" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">%files_dedup</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2900

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2900" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2849

</td>

<td class="new_line diff-line-num" data-linenumber="2901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2901

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2901" class="line" lang="perl">  <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="2850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2850

</td>

<td class="new_line diff-line-num old" data-linenumber="2902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2850" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Checking </span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">... </span><span class="p">";}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="2851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2851

</td>

<td class="new_line diff-line-num old" data-linenumber="2902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2851" class="line" lang="perl">    <span class="nv" style="color: #008080;">&read_details</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="2852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2852

</td>

<td class="new_line diff-line-num old" data-linenumber="2902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2852" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">autoblast</span><span class="p">")</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;"> (</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$autoblast_fileis</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">) </span><span class="p">";}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="2853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2853

</td>

<td class="new_line diff-line-num old" data-linenumber="2902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2853" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">ok</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2902

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2902" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$file</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$files_dedup</span><span class="p">{</span><span class="nv" style="color: #008080;">abs_path</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)}){</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2903

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2903" class="line" lang="perl">      <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">found duplicated entry </span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">, I will ignore it ... </span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2904

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2904" class="line" lang="perl">    <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2905

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2905" class="line" lang="perl">      <span class="nv" style="color: #008080;">$files_dedup</span><span class="p">{</span><span class="nv" style="color: #008080;">abs_path</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)}</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$file</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2906

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2906" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Checking </span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">... </span><span class="p">";}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2907

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2907" class="line" lang="perl">      <span class="nv" style="color: #008080;">&read_details</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2908

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2908" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">autoblast</span><span class="p">")</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;"> (</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$autoblast_fileis</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">) </span><span class="p">";}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2909

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2909" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">ok</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2910

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2910" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2854

</td>

<td class="new_line diff-line-num" data-linenumber="2911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2911

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2911" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2912

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2912" class="line" lang="perl">  <span class="nv" style="color: #008080;">@files</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">values</span><span class="p">(</span><span class="nv" style="color: #008080;">%files_dedup</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2855

</td>

<td class="new_line diff-line-num" data-linenumber="2913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2913

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2913" class="line" lang="perl"><span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2856

</td>

<td class="new_line diff-line-num" data-linenumber="2914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2914

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2914" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2857

</td>

<td class="new_line diff-line-num" data-linenumber="2915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2915

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2915" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">convertUniprotAndNCBI</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2868,9 +2926,10 @@ sub convertUniprotAndNCBI {</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2868

</td>

<td class="new_line diff-line-num" data-linenumber="2926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2926

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2926" class="line" lang="perl"><span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2869

</td>

<td class="new_line diff-line-num" data-linenumber="2927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2927

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2927" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2870

</td>

<td class="new_line diff-line-num" data-linenumber="2928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2928

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2928" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">read_details</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2929

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2929" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2930

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2930" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$from_synteny_call</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2871

</td>

<td class="new_line diff-line-num" data-linenumber="2931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2931

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2931" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">%ids</span><span class="p">;</span>        <span class="c1" style="color: #998; font-style: italic;"># local test for duplicated IDs</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2872

</td>

<td class="new_line diff-line-num" data-linenumber="2932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2932

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2932" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">%genes</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="2873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2873

</td>

<td class="new_line diff-line-num old" data-linenumber="2933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2873" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2874

</td>

<td class="new_line diff-line-num" data-linenumber="2933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2933

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2933" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$test</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2875

</td>

<td class="new_line diff-line-num" data-linenumber="2934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2934

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2934" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$lastgenename</span><span class="o" style="font-weight: 600;">=</span><span class="p">"";</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2876

</td>

<td class="new_line diff-line-num" data-linenumber="2935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2935

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2935" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$cur_gene_is_valid</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2882,6 +2941,8 @@ sub read_details {</td>

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<td class="old_line diff-line-num" data-linenumber="2882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2882

</td>

<td class="new_line diff-line-num" data-linenumber="2941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2941

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2941" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2883

</td>

<td class="new_line diff-line-num" data-linenumber="2942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2942

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2942" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">%isoform_mapping_ncbiuniprot_correction</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># the ncbi uniprot isoforms are not correspoding to the correct ID !</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2884

</td>

<td class="new_line diff-line-num" data-linenumber="2943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2943

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2943" class="line" lang="perl">  </span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2944

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2944" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$found_comma_in_file</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2945

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2945" class="line" lang="perl"></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2885

</td>

<td class="new_line diff-line-num" data-linenumber="2946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2946

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2946" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$did_found_emptyline</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2886

</td>

<td class="new_line diff-line-num" data-linenumber="2947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2947

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2947" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$file</span><span class="p">)</span>    <span class="p">{</span><span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">File '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' not found!</span><span class="p">");}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2887

</td>

<td class="new_line diff-line-num" data-linenumber="2948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2948

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2948" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: #008080;">FASTA</span><span class="p">,"</span><span class="s2" style="color: #d14;"><</span><span class="si" style="color: #d14;">$file</span><span class="p">")</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">Could not open '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">': $!</span><span class="p">");</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2915,7 +2976,6 @@ sub read_details {</td>

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

<td class="old_line diff-line-num" data-linenumber="2915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2915

</td>

<td class="new_line diff-line-num" data-linenumber="2976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2976

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2976" class="line" lang="perl">          <span class="nv" style="color: #008080;">$iso</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/^>//</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2916

</td>

<td class="new_line diff-line-num" data-linenumber="2977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2977

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2977" class="line" lang="perl">          <span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">}</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$iso</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2917

</td>

<td class="new_line diff-line-num" data-linenumber="2978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2978

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2978" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="2918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2918

</td>

<td class="new_line diff-line-num old" data-linenumber="2979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2918" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#print STDERR "DEBUG::1) ".$file." ".$curLine."\n";</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2919

</td>

<td class="new_line diff-line-num" data-linenumber="2979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2979

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2979" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2920

</td>

<td class="new_line diff-line-num" data-linenumber="2980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2980

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2980" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">found isoform '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$curLine</span><span class="s2" style="color: #d14;">' => '</span><span class="si" style="color: #d14;">$iso</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2921

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<td class="new_line diff-line-num" data-linenumber="2981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2981

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<pre style="margin: 0;"> <span id="LC2981" class="line" lang="perl">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2951,10 +3011,18 @@ sub read_details {</td>

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2951

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<td class="new_line diff-line-num" data-linenumber="3011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3011

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<pre style="margin: 0;"> <span id="LC3011" class="line" lang="perl">      <span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/^>//</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2952

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<td class="new_line diff-line-num" data-linenumber="3012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3012

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<pre style="margin: 0;"> <span id="LC3012" class="line" lang="perl">      <span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/\s.*//</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2953

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<td class="new_line diff-line-num" data-linenumber="3013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3013

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<pre style="margin: 0;"> <span id="LC3013" class="line" lang="perl">      <span class="nv" style="color: #008080;">$lastgenename</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2954

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<td class="new_line diff-line-num old" data-linenumber="3014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2954" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$isoform</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"")</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;"># disable for -isoform<span class="idiff left right">, since then the </span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3014

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<pre style="margin: 0;">+<span id="LC3014" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$isoform</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"")</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;"># disable for -isoform</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2955

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<td class="new_line diff-line-num" data-linenumber="3015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3015

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<pre style="margin: 0;"> <span id="LC3015" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$ids</span><span class="p">{</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">}))</span>  <span class="p">{</span><span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">Gene ID '</span><span class="si" style="color: #d14;">$curLine</span><span class="s2" style="color: #d14;">' is defined at least twice in </span><span class="si" style="color: #d14;">$file</span><span class="p">");}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2956

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<td class="new_line diff-line-num" data-linenumber="3016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3016

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<pre style="margin: 0;"> <span id="LC3016" class="line" lang="perl">        <span class="nv" style="color: #008080;">$ids</span><span class="p">{</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$file</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2957

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<td class="new_line diff-line-num" data-linenumber="3017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3017

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<pre style="margin: 0;"> <span id="LC3017" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3018

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<pre style="margin: 0;">+<span id="LC3018" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">index</span><span class="p">(</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">,</span><span class="p">")</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3019

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<pre style="margin: 0;">+<span id="LC3019" class="line" lang="perl">        <span class="c1" style="color: #998; font-style: italic;"># 6.0.32 : check if gene name contains a comma -> this will cause problems with the proteinortho.tsv output (gene cluster speparator)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3020

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<pre style="margin: 0;">+<span id="LC3020" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file_clean</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">abs_path</span> <span class="nv" style="color: #008080;">$file</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3021

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<pre style="margin: 0;">+<span id="LC3021" class="line" lang="perl">        <span class="nv" style="color: #008080;">$file_clean</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/(\.[^.]+)$/_clean$1/</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3022

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3022" class="line" lang="perl">        <span class="nv" style="color: #008080;">$found_comma_in_file</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="2958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3023

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<pre style="margin: 0;">+<span id="LC3023" class="line" lang="perl">        <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> [WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> input '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' contains a gene-name with a comma, this causes problems with the proteinortho.tsv output, I will clean the file ('</span><span class="si" style="color: #d14;">$file_clean</span><span class="s2" style="color: #d14;">') and restart the analysis !!!</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

</td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="3024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3024

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3024" class="line" lang="perl">        <span class="k" style="font-weight: 600;">last</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3025

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3025" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2958

</td>

<td class="new_line diff-line-num" data-linenumber="3026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3026

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3026" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$synteny</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">$genes</span><span class="p">{</span><span class="nv" style="color: #008080;">$curLine</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="2959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2959

</td>

<td class="new_line diff-line-num" data-linenumber="3027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3027

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3027" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2960

</td>

<td class="new_line diff-line-num" data-linenumber="3028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3028

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3028" class="line" lang="perl">      <span class="nv" style="color: #008080;">$cur_gene_is_valid</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2990,6 +3058,35 @@ sub read_details {</td>

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<td class="old_line diff-line-num" data-linenumber="2990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2990

</td>

<td class="new_line diff-line-num" data-linenumber="3058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3058

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3058" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2991

</td>

<td class="new_line diff-line-num" data-linenumber="3059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3059

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3059" class="line" lang="perl">     <span class="p">}</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="2992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2992

</td>

<td class="new_line diff-line-num" data-linenumber="3060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3060

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3060" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3061

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3061" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: #008080;">FASTA</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3062

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3062" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3063

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3063" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$found_comma_in_file</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$from_synteny_call</span><span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3064

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3064" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"># 6.0.32 : replace the , with ; -> write output in a *_clean.* file</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3065

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3065" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file_clean</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">abs_path</span> <span class="nv" style="color: #008080;">$file</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3066

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3066" class="line" lang="perl">    <span class="nv" style="color: #008080;">$file_clean</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/(\.[^.]+)$/_clean$1/</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3067

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3067" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: #008080;">FASTA</span><span class="p">,"</span><span class="s2" style="color: #d14;"><</span><span class="si" style="color: #d14;">$file</span><span class="p">")</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">Could not open '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">': $!</span><span class="p">");</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3068

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3068" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: #008080;">FASTA_CLEAN</span><span class="p">,"</span><span class="s2" style="color: #d14;">></span><span class="si" style="color: #d14;">$file_clean</span><span class="p">")</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">Could not open '</span><span class="si" style="color: #d14;">$file_clean</span><span class="s2" style="color: #d14;">': $!</span><span class="p">");</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3069

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3069" class="line" lang="perl">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: #008080;">FASTA</span><span class="o" style="font-weight: 600;">></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3070

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3070" class="line" lang="perl">      <span class="vg" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[\n\r]+$//g</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3071

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3071" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="sr" style="color: #009926;">/^>/</span><span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3072

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3072" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@arr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="s2" style="color: #d14;"> </span><span class="p">",</span><span class="vg" style="color: #008080;">$_</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3073

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3073" class="line" lang="perl">        <span class="nv" style="color: #008080;">$arr</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="sr" style="color: #009926;">s/,/;/g</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3074

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3074" class="line" lang="perl">        <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">FASTA_CLEAN</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;"> </span><span class="p">",</span><span class="nv" style="color: #008080;">@arr</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3075

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3075" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="vg" style="color: #008080;">$_</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3076

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3076" class="line" lang="perl">        <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">FASTA_CLEAN</span> <span class="p">"</span><span class="si" style="color: #d14;">$_</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3077

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3077" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3078

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3078" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3079

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3079" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: #008080;">FASTA</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3080

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3080" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: #008080;">FASTA_CLEAN</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3081

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3081" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span><span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3082

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3082" class="line" lang="perl">      <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> [WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> Restarting the indices generation.</span><span class="si" style="color: #d14;">$NC</span><span class="p">");</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3083

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3083" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@arr</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="nv" style="color: #008080;">$file_clean</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3084

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3084" class="line" lang="perl">      <span class="nv" style="color: #008080;">&generate_indices</span><span class="p">(</span><span class="nv" style="color: #008080;">@arr</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3085

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3085" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3086

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3086" class="line" lang="perl">    <span class="vg" style="color: #008080;">$_</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="nv" style="color: #008080;">$file</span> <span class="ow" style="font-weight: 600;">and</span> <span class="vg" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$file_clean</span> <span class="k" style="font-weight: 600;">for</span> <span class="nv" style="color: #008080;">@files</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3087

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3087" class="line" lang="perl">    <span class="vg" style="color: #008080;">$_</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="nv" style="color: #008080;">$file</span> <span class="ow" style="font-weight: 600;">and</span> <span class="vg" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$file_clean</span> <span class="k" style="font-weight: 600;">for</span> <span class="nv" style="color: #008080;">@files_cleanup</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3088

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3088" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">goto</span> <span class="nv" style="color: #008080;">RESTART_check_files</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3089

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3089" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2993

</td>

<td class="new_line diff-line-num" data-linenumber="3090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3090

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3090" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2994

</td>

<td class="new_line diff-line-num" data-linenumber="3091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3091

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3091" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$isoform</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">uniprot</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$isoform</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">ncbi</span><span class="p">"){</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2995

</td>

<td class="new_line diff-line-num" data-linenumber="3092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3092

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3092" class="line" lang="perl">    <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$key</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: #008080;">%isoform_mapping</span><span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3032,9 +3129,9 @@ sub read_details {</td>

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<td class="old_line diff-line-num" data-linenumber="3032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3032

</td>

<td class="new_line diff-line-num" data-linenumber="3129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3129

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3129" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">exists</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode_pendant</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$blastmode</span><span class="p">})</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$restart_counter</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">2</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;"># only for step = 0 and step 1 you can do a rerun else the DB are missing</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3033

</td>

<td class="new_line diff-line-num" data-linenumber="3130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3130

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3130" class="line" lang="perl">        <span class="nv" style="color: #008080;">$blastmode</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$blastmode_pendant</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$blastmode</span><span class="p">};</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3034

</td>

<td class="new_line diff-line-num" data-linenumber="3131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3131

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3131" class="line" lang="perl">        <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">!!!</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> Switching now to </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> and restarting...</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="3035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3035

</td>

<td class="new_line diff-line-num old" data-linenumber="3132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3035" class="line" lang="perl">      <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Press 'strg+c' to prevent me from proceeding or wait 10 seconds to continue...</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">!!!</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="3036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3036

</td>

<td class="new_line diff-line-num old" data-linenumber="3132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3036" class="line" lang="perl">       <span class="nb" style="color: #0086b3;">sleep</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="3037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3037

</td>

<td class="new_line diff-line-num old" data-linenumber="3132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3037" class="line" lang="perl">      <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Well then, proceeding...</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="3038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3132

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3132" class="line" lang="perl">      <span class="idiff left right">  </span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Press 'strg+c' to prevent me from proceeding or wait 10 seconds to continue...</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">!!!</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="3038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3133

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3133" class="line" lang="perl">       <span class="idiff left right"> </span><span class="nb" style="color: #0086b3;">sleep</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="3038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3134

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3134" class="line" lang="perl">      <span class="idiff left right">  </span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Well then, proceeding...</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="3038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3038

</td>

<td class="new_line diff-line-num" data-linenumber="3135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3135

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3135" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">goto</span> <span class="nv" style="color: #008080;">RESTART</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="3039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3039

</td>

<td class="new_line diff-line-num" data-linenumber="3136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3136

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3136" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="3040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3040

</td>

<td class="new_line diff-line-num" data-linenumber="3137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3137

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3137" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3060,7 +3157,6 @@ sub read_details {</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="3060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3060

</td>

<td class="new_line diff-line-num" data-linenumber="3157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3157

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3157" class="line" lang="perl">      <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The algorithm (-p=</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">) does not support the given input files (use --force to skip this behaviour)...</span><span class="p">");</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="3061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3061

</td>

<td class="new_line diff-line-num" data-linenumber="3158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3158

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3158" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="3062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3062

</td>

<td class="new_line diff-line-num" data-linenumber="3159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3159

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3159" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="3063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3063

</td>

<td class="new_line diff-line-num old" data-linenumber="3160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3063" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: #008080;">FASTA</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="3064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3064

</td>

<td class="new_line diff-line-num" data-linenumber="3160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3160

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3160" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="3065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3065

</td>

<td class="new_line diff-line-num" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3161

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3161" class="line" lang="perl">  <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: #008080;">$synteny</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span><span class="p">;}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="3066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3066

</td>

<td class="new_line diff-line-num" data-linenumber="3162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3162

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3162" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3074,17 +3170,26 @@ sub read_details {</td>

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

<td class="old_line diff-line-num" data-linenumber="3074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3074

</td>

<td class="new_line diff-line-num" data-linenumber="3170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3170

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3170" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"># e.g. NC_009925.1  RefSeq  CDS 9275  10096 . - 0 ID=cds8;Name=YP_001514414.1;Parent=gene9;Dbxref=Genbank:YP_001514414.1,GeneID:5678848;gbkey=CDS;product=signal peptide peptidase SppA;protein_id=YP_001514414.1;transl_table=11</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="3075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3075

</td>

<td class="new_line diff-line-num" data-linenumber="3171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3171

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3171" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@col</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\t+/</span><span class="p">,</span><span class="vg" style="color: #008080;">$_</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="3076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3076

</td>

<td class="new_line diff-line-num" data-linenumber="3172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3172

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3172" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$col</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">CDS</span><span class="p">")</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="3077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3077

</td>

<td class="new_line diff-line-num old" data-linenumber="3173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3077" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$col</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/Name=([^;]+)/i</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$genes</span><span class="p">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">}))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="3078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3078

</td>

<td class="new_line diff-line-num old" data-linenumber="3173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3078" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">delete</span> <span class="nv" style="color: #008080;">$genes</span><span class="p">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">};</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="3079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3079

</td>

<td class="new_line diff-line-num old" data-linenumber="3173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3079" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#     if (!$test) {$coordinates{$1} = "$col[0]\t$col[6]\t$col[3]";} # store</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="3080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3080

</td>

<td class="new_line diff-line-num old" data-linenumber="3173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3080" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$col</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">+</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">$coordinates</span><span class="p">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[6]</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[3]</span><span class="p">";}</span> <span class="c1" style="color: #998; font-style: italic;"># store</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3081

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<td class="new_line diff-line-num old" data-linenumber="3173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3081" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$col</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">-</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">$coordinates</span><span class="p">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[6]</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[4]</span><span class="p">";}</span> <span class="c1" style="color: #998; font-style: italic;"># store</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3173

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<pre style="margin: 0;">+<span id="LC3173" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$col</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/Name=([^;]+)/i</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3174

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<pre style="margin: 0;">+<span id="LC3174" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$gene_nam</span><span class="o" style="font-weight: 600;">=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3175

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<pre style="margin: 0;">+<span id="LC3175" class="line" lang="perl">      <span class="nv" style="color: #008080;">$gene_nam</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/,/;/g</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># 6.0.32 ,->;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3176

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<pre style="margin: 0;">+<span id="LC3176" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$genes</span><span class="p">{</span><span class="nv" style="color: #008080;">$gene_nam</span><span class="p">})){</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3177

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<pre style="margin: 0;">+<span id="LC3177" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">delete</span> <span class="nv" style="color: #008080;">$genes</span><span class="p">{</span><span class="nv" style="color: #008080;">$gene_nam</span><span class="p">};</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3178

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<pre style="margin: 0;">+<span id="LC3178" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#       if (!$test) {$coordinates{$1} = "$col[0]\t$col[6]\t$col[3]";} # store</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3179

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3179" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$col</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">+</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">$coordinates</span><span class="p">{</span><span class="nv" style="color: #008080;">$gene_nam</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[6]</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[3]</span><span class="p">";}</span> <span class="c1" style="color: #998; font-style: italic;"># store</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3180

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3180" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$col</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">-</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">$coordinates</span><span class="p">{</span><span class="nv" style="color: #008080;">$gene_nam</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[6]</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[4]</span><span class="p">";}</span> <span class="c1" style="color: #998; font-style: italic;"># store</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3181

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<pre style="margin: 0;">+<span id="LC3181" class="line" lang="perl">        <span class="k" style="font-weight: 600;">next</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3182

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3182" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

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3082

</td>

<td class="new_line diff-line-num" data-linenumber="3183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3183

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<pre style="margin: 0;"> <span id="LC3183" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="3083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3083

</td>

<td class="new_line diff-line-num old" data-linenumber="3184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3083" class="line" lang="perl">    <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$col</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/ID=([^;]+)/i</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$genes</span><span class="p">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">}))</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3084

</td>

<td class="new_line diff-line-num old" data-linenumber="3184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3084" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">delete</span> <span class="nv" style="color: #008080;">$genes</span><span class="p">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">};</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3085

</td>

<td class="new_line diff-line-num old" data-linenumber="3184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3085" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#     if (!$test) {$coordinates{$1} = "$col[0]\t$col[6]\t$col[3]";} # store</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3086

</td>

<td class="new_line diff-line-num old" data-linenumber="3184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3086" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$col</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">+</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">$coordinates</span><span class="p">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[6]</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[3]</span><span class="p">";}</span> <span class="c1" style="color: #998; font-style: italic;"># store</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3087

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<td class="new_line diff-line-num old" data-linenumber="3184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3087" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$col</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">-</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">$coordinates</span><span class="p">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[6]</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[4]</span><span class="p">";}</span> <span class="c1" style="color: #998; font-style: italic;"># store</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3184

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3184" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$col</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/ID=([^;]+)/i</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3185

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3185" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$gene_nam</span><span class="o" style="font-weight: 600;">=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3186

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3186" class="line" lang="perl">      <span class="nv" style="color: #008080;">$gene_nam</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/,/;/g</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># 6.0.32 ,->;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3187

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3187" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$genes</span><span class="p">{</span><span class="nv" style="color: #008080;">$gene_nam</span><span class="p">})){</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3188

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3188" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">delete</span> <span class="nv" style="color: #008080;">$genes</span><span class="p">{</span><span class="nv" style="color: #008080;">$gene_nam</span><span class="p">};</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="3088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3189

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3189" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#       if (!$test) {$coordinates{$1} = "$col[0]\t$col[6]\t$col[3]";} # store</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3190

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3190" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$col</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">+</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">$coordinates</span><span class="p">{</span><span class="nv" style="color: #008080;">$gene_nam</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[6]</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[3]</span><span class="p">";}</span> <span class="c1" style="color: #998; font-style: italic;"># store</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="3088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3191

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3191" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$col</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">-</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">$coordinates</span><span class="p">{</span><span class="nv" style="color: #008080;">$gene_nam</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[6]</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">$col</span><span class="s2" style="color: #d14;">[4]</span><span class="p">";}</span> <span class="c1" style="color: #998; font-style: italic;"># store</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3192

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3192" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3088

</td>

<td class="new_line diff-line-num" data-linenumber="3193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3193

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3193" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3089

</td>

<td class="new_line diff-line-num" data-linenumber="3194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3194

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3194" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3090

</td>

<td class="new_line diff-line-num" data-linenumber="3195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3195

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3195" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: #008080;">GFF</span><span class="p">);</span></span>

</pre>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3105,7 +3210,7 @@ sub Error {</td>

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<td class="old_line diff-line-num" data-linenumber="3105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3105

</td>

<td class="new_line diff-line-num" data-linenumber="3210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3210

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3210" class="line" lang="perl"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3106

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<td class="new_line diff-line-num" data-linenumber="3211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3211

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<pre style="margin: 0;"> <span id="LC3211" class="line" lang="perl">  <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n\n</span><span class="si" style="color: #d14;">$RED</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">[Error]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="vg" style="color: #008080;">$_</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="p">"</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3107

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<td class="new_line diff-line-num" data-linenumber="3212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3212

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3212" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3108

</td>

<td class="new_line diff-line-num old" data-linenumber="3213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3108" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$_</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">I need at least two files to compare something!</span><span class="p">"){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;"><span class="idiff left">If you cannot solve this error, please send a report to incoming+</span>paulklemm<span class="idiff">-phd-</span>proteinortho<span class="idiff">-7278443-issue-</span></span><span class="se" style="color: #d14;"><span class="idiff">\@</span></span><span class="s2" style="color: #d14;"><span class="idiff">incoming.gitlab.com including the parameter-vector above or visit https://gitlab.com/</span>paulklemm<span class="idiff">_PHD/</span>proteinortho<span class="idiff right">/wikis/Error%20Codes for more help.</span></span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Further more all mails to lechner</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">staff.uni-marburg.de are welcome</span><span class="se" style="color: #d14;">\n\n\n</span><span class="p">";}</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="3109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3213

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3213" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$_</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">I need at least two files to compare something!</span><span class="p">"){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;"><span class="idiff left">Please visit the proteinortho-wiki, where the most common errors are documented:</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">https://gitlab.com/</span>paulklemm<span class="idiff">_PHD/</span>proteinortho<span class="idiff">/wikis/Error%20Codes</span></span><span class="se" style="color: #d14;"><span class="idiff">\n\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">If you cannot solve this error, please file a report (including the input files, the error code and the above 'Parameter-vector'):</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s2" style="color: #d14;"><span class="idiff">incoming+</span>paulklemm<span class="idiff">-phd-</span>proteinortho<span class="idiff">-7278443-issue-</span></span><span class="se" style="color: #d14;"><span class="idiff">\@</span></span><span class="s2" style="color: #d14;"><span class="idiff">incoming.gitlab.com</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span>\n</span><span class="s2" style="color: #d14;">Further more all mails to lechner</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">staff.uni-marburg.de are welcome<span class="idiff right">.</span></span><span class="se" style="color: #d14;">\n\n\n</span><span class="p">";}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3109

</td>

<td class="new_line diff-line-num" data-linenumber="3214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3214

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3214" class="line" lang="perl"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3110

</td>

<td class="new_line diff-line-num" data-linenumber="3215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3215

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3215" class="line" lang="perl">  <span class="nv" style="color: #008080;">&reset_locale</span><span class="p">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3111

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<td class="new_line diff-line-num" data-linenumber="3216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3216

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3216" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$keep</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$tmp_path</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/\/proteinortho_cache_[^\/]+\d*\/$/</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">1</span> <span class="p">){</span><span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">rm -r </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> >/dev/null 2>&1</span><span class="p">");}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3120,6 +3225,10 @@ sub gff4fasta {</td>

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<td class="old_line diff-line-num" data-linenumber="3120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3120

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<td class="new_line diff-line-num" data-linenumber="3225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3225

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3225" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$gff</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: #008080;">$gff</span><span class="p">;}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3121

</td>

<td class="new_line diff-line-num" data-linenumber="3226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3226

</td>

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<pre style="margin: 0;"> <span id="LC3226" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$gff</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">3</span><span class="p">")</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: #008080;">$gff</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">3</span><span class="p">";}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3122

</td>

<td class="new_line diff-line-num" data-linenumber="3227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3227

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3227" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="3123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3228

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3228" class="line" lang="perl">  <span class="nv" style="color: #008080;">$gff</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/_clean\.gff$/.gff/</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="3123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3229

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3229" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$gff</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: #008080;">$gff</span><span class="p">;}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="3123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3230

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3230" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$gff</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">3</span><span class="p">")</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: #008080;">$gff</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">3</span><span class="p">";}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="3123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3231

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3231" class="line" lang="perl"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3123

</td>

<td class="new_line diff-line-num" data-linenumber="3232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3232

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3232" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$ncbi_gff</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gff</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3124

</td>

<td class="new_line diff-line-num" data-linenumber="3233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3233

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3233" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ncbi_gff</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/_cds_from//</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3125

</td>

<td class="new_line diff-line-num" data-linenumber="3234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3234

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3234" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$ncbi_gff</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: #008080;">$ncbi_gff</span><span class="p">;}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3154,8 +3263,8 @@ sub get_po_path {</td>

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<td class="old_line diff-line-num" data-linenumber="3154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3154

</td>

<td class="new_line diff-line-num" data-linenumber="3263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3263

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3263" class="line" lang="perl">      <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="si" style="color: #d14;">$binpath</span><span class="s2" style="color: #d14;">/</span><span class="p">";</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3155

</td>

<td class="new_line diff-line-num" data-linenumber="3264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3264

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3264" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Detected </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$tmppath</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="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3156

</td>

<td class="new_line diff-line-num" data-linenumber="3265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3265

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3265" class="line" lang="perl">    <span class="p">}</span><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="3157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3157

</td>

<td class="new_line diff-line-num old" data-linenumber="3266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3157" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$p</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">wh<span class="idiff left right">ereis</span> proteinortho_clustering</span><span class="p">`;</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="3158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3158

</td>

<td class="new_line diff-line-num old" data-linenumber="3266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3158" class="line" lang="perl">      <span class="nv" style="color: #008080;">$p</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/^<span class="idiff left right">proteinortho_clustering:  *</span>([^ ]+)\/proteinortho_clustering.*$/$1/</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="3159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3266

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3266" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$p</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">wh<span class="idiff left right">ich</span> proteinortho_clustering</span><span class="p">`;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="3159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3267

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3267" class="line" lang="perl">      <span class="nv" style="color: #008080;">$p</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/^([^ ]+)\/proteinortho_clustering.*$/$1/</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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3159

</td>

<td class="new_line diff-line-num" data-linenumber="3268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3268

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<pre style="margin: 0;"> <span id="LC3268" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">chomp</span><span class="p">(</span><span class="nv" style="color: #008080;">$p</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3160

</td>

<td class="new_line diff-line-num" data-linenumber="3269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3269

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<pre style="margin: 0;"> <span id="LC3269" class="line" lang="perl">      <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$p</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3161

</td>

<td class="new_line diff-line-num" data-linenumber="3270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3270

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<pre style="margin: 0;"> <span id="LC3270" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Detected (PATH enviroment variable)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="e88e2072d8bed1edd8ac79e979262281cfe9549b">

<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/50d748b5c10ee4ec1db1c0ec09e45d0f0dddb9cf#e88e2072d8bed1edd8ac79e979262281cfe9549b"><strong>src/.gitlab-ci.yml</strong></a>

<hr>

<table class="code white" style="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(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,7 +13,7 @@ gcc-latest-manyoptions-together:</td>

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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="yaml">  <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">test-precompiled-bins</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="yaml">  <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

</td>

<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">echo "installing diamond"</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

</td>

<td class="new_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz<span class="idiff left right"> 2>/dev/null</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

</td>

<td class="new_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC17" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">tar xzf diamond-linux64.tar.gz</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

</td>

<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cp diamond $HOME</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

</td>

<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">export PATH="$PATH:$HOME"</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,7 +27,7 @@ gcc-latest-someoptions-one-by-one:</td>

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<td class="old_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

27

</td>

<td class="new_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

27

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC27" class="line" lang="yaml">  <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">test-precompiled-bins</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

28

</td>

<td class="new_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

28

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC28" class="line" lang="yaml">  <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

29

</td>

<td class="new_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

29

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC29" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">echo "installing diamond"</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

30

</td>

<td class="new_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC30" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

30

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz<span class="idiff left right"> 2>/dev/null</span></span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

31

</td>

<td class="new_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

31

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC31" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">tar xzf diamond-linux64.tar.gz</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cp diamond $HOME</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">export PATH="$PATH:$HOME"</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -61,17 +61,17 @@ gcc-latest-all-p:</td>

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<td class="old_line diff-line-num" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="yaml">  <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">export CWD=$(pwd)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">echo "installing last"</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://last.cbrc.jp/last-982.zip && unzip last*zip 2>/dev/null && cd last*/ && make && cp src/last* $HOME</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://last.cbrc.jp/last-982.zip <span class="idiff left right">2>/dev/null </span>&& unzip last*zip 2>/dev/null && cd last*/ && make && cp src/last* $HOME</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cd $CWD && echo "installing usearch"</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">curl https://drive5.com/cgi-bin/upload3.py?license=2019070410321731111 --output $HOME/usearch && chmod +x $HOME/usearch</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cd $CWD && echo "installing mmseqs2"</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">git clone https://github.com/soedinglab/MMseqs2 && cd MMs* && cmake . && make && cp src/mmseqs $HOME && cd ..</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cd $CWD && echo "installing blat"</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/blat/blat && cp blat $HOME && chmod +x $HOME/blat</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/blat/blat <span class="idiff left right">2>/dev/null </span>&& cp blat $HOME && chmod +x $HOME/blat</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cd $CWD && echo "installing topaz"</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">git clone https://github.com/ajm/topaz && cd topaz/src && make && cp topaz $HOME && cd ../..</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cd $CWD && echo "installing diamond"</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz && tar xzf diamond-linux64.tar.gz && cp diamond $HOME</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz <span class="idiff left right">2>/dev/null </span>&& tar xzf diamond-linux64.tar.gz && cp diamond $HOME</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">export PATH="$PATH:$HOME"</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">echo "start proteinortho tests"</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

77

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<td class="new_line diff-line-num" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">gcc --version</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -87,7 +87,7 @@ gcc-latest-diamond:</td>

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<td class="old_line diff-line-num" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

87

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<td class="new_line diff-line-num" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

87

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="yaml">  <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">test-precompiled-bins</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

88

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="yaml">  <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

89

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<td class="new_line diff-line-num" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">echo "installing diamond"</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

90

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<td class="new_line diff-line-num old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz<span class="idiff left right"> 2>/dev/null</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

91

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<td class="new_line diff-line-num" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

91

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">tar xzf diamond-linux64.tar.gz</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

92

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<td class="new_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

92

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cp diamond $HOME</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

93

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<td class="new_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">export PATH="$PATH:$HOME"</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -103,7 +103,7 @@ nolapack-gcc-latest:</td>

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<td class="old_line diff-line-num" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

103

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<td class="new_line diff-line-num" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

103

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="yaml">  <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">recompile-and-test</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

104

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<td class="new_line diff-line-num" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

104

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="yaml">  <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

105

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<td class="new_line diff-line-num" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">echo "installing diamond"</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

106

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<td class="new_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

106

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz<span class="idiff left right"> 2>/dev/null</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

107

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<td class="new_line diff-line-num" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

107

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">tar xzf diamond-linux64.tar.gz</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

108

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<td class="new_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

108

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cp diamond $HOME</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">export PATH="$PATH:$HOME"</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -126,7 +126,7 @@ nolapack-gcc-latest:</td>

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<td class="old_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - make</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - cp topaz $HOME</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - echo "installing diamond"</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz<span class="idiff left right"> 2>/dev/null</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - tar xzf diamond-linux64.tar.gz</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - cp diamond $HOME</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - export PATH="$PATH:$HOME"</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -149,7 +149,7 @@ ubuntu-latest0:</td>

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<td class="new_line diff-line-num" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cp topaz $HOME</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cd ../..</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">echo "installing diamond"</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC152" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz<span class="idiff left right"> 2>/dev/null</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">tar xzf diamond-linux64.tar.gz</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cp diamond $HOME</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">export PATH="$PATH:$HOME"</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -171,7 +171,7 @@ ubuntu-latest:</td>

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<td class="old_line diff-line-num" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cp topaz $HOME</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

172

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<td class="new_line diff-line-num" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

172

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cd ../..</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

173

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<td class="new_line diff-line-num" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

173

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">echo "installing diamond"</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

174

</td>

<td class="new_line diff-line-num old" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC174" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

174

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz<span class="idiff left right"> 2>/dev/null</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

175

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<td class="new_line diff-line-num" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

175

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">tar xzf diamond-linux64.tar.gz</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

176

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<td class="new_line diff-line-num" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

176

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cp diamond $HOME</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

177

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<td class="new_line diff-line-num" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

177

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">export PATH="$PATH:$HOME"</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -194,7 +194,7 @@ debian-latest:</td>

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<td class="old_line diff-line-num" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

194

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<td class="new_line diff-line-num" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

194

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<pre style="margin: 0;"> <span id="LC194" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">make</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

195

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<td class="new_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

195

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cp topaz $HOME</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

196

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<td class="new_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

196

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">echo "installing diamond"</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

197

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<td class="new_line diff-line-num old" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC197" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

197

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz<span class="idiff left right"> 2>/dev/null</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

198

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<td class="new_line diff-line-num" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

198

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<pre style="margin: 0;"> <span id="LC198" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">tar xzf diamond-linux64.tar.gz</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

199

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<td class="new_line diff-line-num" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

199

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cp diamond $HOME</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

200

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<td class="new_line diff-line-num" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

200

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">export PATH="$PATH:$HOME"</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -224,12 +224,12 @@ debian-latest:</td>

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<td class="old_line diff-line-num" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

224

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<td class="new_line diff-line-num" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

224

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<pre style="margin: 0;"> <span id="LC224" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - yum -y install python</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

225

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<td class="new_line diff-line-num" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

225

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<pre style="margin: 0;"> <span id="LC225" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - yum -y install ncbi-blast+</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

226

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<td class="new_line diff-line-num" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

226

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - cpan Thread::Queue</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

227

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<td class="new_line diff-line-num old" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC227" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast*-x64-linux.tar.gz</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast*-x64-linux.tar.gz<span class="idiff left right"> 2>/dev/null</span></span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

228

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<td class="new_line diff-line-num" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

228

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - tar -xzvf ncbi-blast*-x64-linux.tar.gz</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

229

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<td class="new_line diff-line-num" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

229

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - cp ncbi-blast*/bin/blastp $HOME</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

230

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<td class="new_line diff-line-num" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

230

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - cp ncbi-blast*/bin/makeblastdb $HOME</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

231

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<td class="new_line diff-line-num" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

231

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - echo "installing diamond"</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

232

</td>

<td class="new_line diff-line-num old" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC232" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

232

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz<span class="idiff left right"> 2>/dev/null</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

233

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<td class="new_line diff-line-num" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

233

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - tar xzf diamond-linux64.tar.gz</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

234

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<td class="new_line diff-line-num" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

234

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - cp diamond $HOME</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

235

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<td class="new_line diff-line-num" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - export PATH="$PATH:$HOME"</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -247,12 +247,12 @@ debian-latest:</td>

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<td class="old_line diff-line-num" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

247

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<td class="new_line diff-line-num" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

247

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - yum -y install which</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

248

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<td class="new_line diff-line-num" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

248

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - yum -y install wget</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

249

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<td class="new_line diff-line-num" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

249

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - yum -y install gcc-gfortran python3 atlas atlas-devel lapack blas</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

250

</td>

<td class="new_line diff-line-num old" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC250" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast*-x64-linux.tar.gz</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast*-x64-linux.tar.gz<span class="idiff left right"> 2>/dev/null</span></span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

251

</td>

<td class="new_line diff-line-num" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

251

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC251" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - tar -xzvf ncbi-blast*-x64-linux.tar.gz</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

252

</td>

<td class="new_line diff-line-num" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

252

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - cp ncbi-blast*/bin/blastp $HOME</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

253

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<td class="new_line diff-line-num" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

253

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - cp ncbi-blast*/bin/makeblastdb $HOME</span></span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - echo "installing diamond"</span></span>

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<td class="old_line diff-line-num old" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC255" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz<span class="idiff left right"> 2>/dev/null</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - tar xzf diamond-linux64.tar.gz</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - cp diamond $HOME</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - export PATH="$PATH:$HOME"</span></span>

</pre>

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<br>

</li>

<li id="3439148ea7017354388f7c55043cc84986c1c394">

<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/50d748b5c10ee4ec1db1c0ec09e45d0f0dddb9cf#3439148ea7017354388f7c55043cc84986c1c394"><strong>src/proteinortho_grab_proteins.pl</strong></a>

<hr>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,9 +27,9 @@</td>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># </span></span>

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<td class="old_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @author Paul Klemm</span></span>

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<td class="old_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @email klemmp@staff.uni-marburg.de</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @company Bioinformatics, University of <span class="idiff left right">Leipzi</span>g</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @version <span class="idiff left right">6</span></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @date 2-1<span class="idiff left right">0</span>-2021</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @company Bioinformatics, University of <span class="idiff left right">Marbur</span>g</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @version <span class="idiff left right">7</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @date 2<span class="idiff left">3</span>-1<span class="idiff right">2</span>-2021</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<td class="old_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>

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<td class="old_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="perl"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,6 +39,7 @@ use threads::shared;</td>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">POSIX</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">File::</span><span class="nv" style="color: #008080;">Basename</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Thread::</span><span class="nv" style="color: #008080;">Queue</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">Cwd</span> <span class="p">'</span><span class="s1" style="color: #d14;">abs_path</span><span class="p">';</span></span>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$QUEUE</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Thread::</span><span class="nv" style="color: #008080;">Queue</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">();</span>    <span class="c1" style="color: #998; font-style: italic;"># A new empty queue</span></span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$usage</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><<'ENDUSAGE';</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -142,7 +143,15 @@ for(my $v = 0 ; $v < scalar @ARGV_copy ; $v++){</td>

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?exact$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$exact</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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<pre style="margin: 0;"> <span id="LC144" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^-.+/</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$usage</span><span class="p">;</span> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">ERROR: invalid option </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">!</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span><span class="nb" style="color: #0086b3;">exit</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" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$query</span><span class="p">)){</span><span class="nv" style="color: #008080;">$query</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">];}</span></span>

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<td class="new_line diff-line-num old" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="nv" style="color: #008080;">$ARGV_copyiddone</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</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 class="nv" style="color: #008080;">$ARGV_copyiddone_counter</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 new" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="perl"> <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="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="perl">         <span class="c1" style="color: #998; font-style: italic;"># 6.0.32 replace files if there is a *_clean* present</span></span>

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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="perl">         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]){</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file_clean</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">abs_path</span> <span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="perl">                 <span class="nv" style="color: #008080;">$file_clean</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/(\.[^.]+)$/_clean$1/</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$file_clean</span><span class="p">){</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$file_clean</span><span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="perl">         <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="perl">         <span class="nv" style="color: #008080;">$ARGV_copyiddone</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</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 class="nv" style="color: #008080;">$ARGV_copyiddone_counter</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="perl"> <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="perl"><span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$help</span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="perl">    <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$usage</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -223,6 +232,10 @@ unless(open(my $FH,'<',$query)) {</td>

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<td class="new_line diff-line-num" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$sp</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">])</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$sp</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="perl">                 <span class="nv" style="color: #008080;">$sp</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/^\(//</span><span class="p">;</span><span class="nv" style="color: #008080;">$sp</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/\)$//</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@arr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="s2" style="color: #d14;"> </span><span class="p">",</span><span class="nv" style="color: #008080;">$sp</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;"># 6.0.32 , -> ; </span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="perl">         <span class="nv" style="color: #008080;">$arr</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="sr" style="color: #009926;">s/,/;/g</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="perl">         <span class="nv" style="color: #008080;">$sp</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;"> </span><span class="p">",</span><span class="nv" style="color: #008080;">@arr</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

238

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="perl">                 <span class="nv" style="color: #008080;">$qdata</span><span class="p">{"</span><span class="s2" style="color: #d14;">STDIN</span><span class="p">"}{</span><span class="nv" style="color: #008080;">$sp</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]}</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$sp</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">];</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="perl">                 <span class="nv" style="color: #008080;">$genecounter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="perl">         <span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -335,7 +348,11 @@ sub worker {</td>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="perl">                                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@arr</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 class="nv" style="color: #008080;">$genename</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$arr</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];}</span></span>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="perl">                                 <span class="nv" style="color: #008080;">$genename</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/^>//</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC350" class="line" lang="perl"></span>

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<td class="old_line diff-line-num old" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC338" class="line" lang="perl">                                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$basename</span><span class="p">}{</span><span class="nv" style="color: #008080;">$genename</span><span class="p">}){</span></span>

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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC351" class="line" lang="perl">                                 <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@arr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="s2" style="color: #d14;"> </span><span class="p">",</span><span class="nv" style="color: #008080;">$genename</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;"># 6.0.32 , -> ; </span></span>

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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC352" class="line" lang="perl">                         <span class="nv" style="color: #008080;">$arr</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="sr" style="color: #009926;">s/,/;/g</span><span class="p">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC353" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$genename_no_comma</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;"> </span><span class="p">",</span><span class="nv" style="color: #008080;">@arr</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC354" class="line" lang="perl">                         </span>

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<td class="new_line diff-line-num new" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC355" class="line" lang="perl">                                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$basename</span><span class="p">}{</span><span class="nv" style="color: #008080;">$genename_no_comma</span><span class="p">}){</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC356" class="line" lang="perl">                                 </span>

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<pre style="margin: 0;"> <span id="LC357" class="line" lang="perl">                                         <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC358" class="line" lang="perl">                                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$source</span><span class="p">){</span><span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$basename</span><span class="p">;}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -355,10 +372,13 @@ sub worker {</td>

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<pre style="margin: 0;"> <span id="LC372" class="line" lang="perl">                                                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$filename</span><span class="p">}{</span><span class="nv" style="color: #008080;">$key</span><span class="p">}){</span><span class="k" style="font-weight: 600;">next</span><span class="p">}</span></span>

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<td class="new_line diff-line-num" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC373" class="line" lang="perl"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC374" class="line" lang="perl">                                                 <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$regexv</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$key</span><span class="p">;</span> </span>

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<td class="old_line diff-line-num new" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

375

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<pre style="margin: 0;">+<span id="LC375" class="line" lang="perl">                                         </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

358

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<td class="new_line diff-line-num" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

376

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<pre style="margin: 0;"> <span id="LC376" class="line" lang="perl">                                                 <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$curLine_test</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$curLine</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

359

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<td class="new_line diff-line-num old" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC359" class="line" lang="perl"><span class="idiff left right">                                                  </span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

377

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC377" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

360

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<td class="new_line diff-line-num" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

378

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<pre style="margin: 0;"> <span id="LC378" class="line" lang="perl">                                                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$doregex</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$exact</span><span class="p">){</span><span class="nv" style="color: #008080;">$regexv</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">quotemeta</span><span class="p">(</span><span class="nv" style="color: #008080;">$regexv</span><span class="p">);}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

361

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<td class="new_line diff-line-num" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

379

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC379" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

380

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<pre style="margin: 0;">+<span id="LC380" class="line" lang="perl">                                                 <span class="nv" style="color: #008080;">$regexv</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/;/[,;]/g</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># 6.0.32 , -> ; </span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

381

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC381" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

362

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<td class="new_line diff-line-num" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

382

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC382" class="line" lang="perl">                                                 <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$test_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

363

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<td class="new_line diff-line-num" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

383

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC383" class="line" lang="perl">                                                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$exact</span> <span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

364

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<td class="new_line diff-line-num" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

384

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC384" class="line" lang="perl">                                                         </span>

</pre>

</td>

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<br>

</li>

<li id="b449ded4202264f363300e737ee12e8592179216">

<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/50d748b5c10ee4ec1db1c0ec09e45d0f0dddb9cf#b449ded4202264f363300e737ee12e8592179216"><strong>test/C.faa</strong></a>

<hr>

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<td class="old_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1

</td>

<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">>C_10</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>C_10<span class="idiff left right">,test</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">VVLCRYEIGGLAQVLDTQFDMYTNCHKMCSADSQVTYKEAANLTARVTTDRQKEPLTGGY</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

</td>

<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">HGAKLGFLGCSLLRSRDYGYPEQNFHAKTDLFALPMGDHYCGDEGSGNAYLCDFDNQYGR</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

</td>

<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">SVRSPLKKLLGFGYNPTYGKSALGDELRLGLVFREEFRKINKALLTGGANVVKAGVSYKD</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="775bfcb5ef827787daeffc1708e26d3be7407847">

<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/50d748b5c10ee4ec1db1c0ec09e45d0f0dddb9cf#775bfcb5ef827787daeffc1708e26d3be7407847"><strong>test/C.gff</strong></a>

<hr>

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

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -207,7 +207,7 @@ gi|12345678|ref|NC_012345.1|       sim     CDS     206     206     .       +       .       ID=C_32;</td>

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<td class="old_line diff-line-num" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

207

</td>

<td class="new_line diff-line-num" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

207

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="plaintext">gi|12345678|ref|NC_012345.1|        sim     CDS     207     207     .       +       .       ID=C_33;</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

208

</td>

<td class="new_line diff-line-num" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

208

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC208" class="line" lang="plaintext">gi|12345678|ref|NC_012345.1|        sim     CDS     208     208     .       +       .       ID=C_34;</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

209

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<td class="new_line diff-line-num" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

209

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC209" class="line" lang="plaintext">gi|12345678|ref|NC_012345.1|        sim     CDS     209     209     .       +       .       ID=C_9;</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

210

</td>

<td class="new_line diff-line-num old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC210" class="line" lang="plaintext">gi|12345678|ref|NC_012345.1|        sim     CDS     210     210     .       +       .       ID=C_10;</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

210

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">gi|12345678|ref|NC_012345.1|        sim     CDS     210     210     .       +       .       ID=C_10<span class="idiff left right">,test</span>;</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

211

</td>

<td class="new_line diff-line-num" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

211

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC211" class="line" lang="plaintext">gi|12345678|ref|NC_012345.1|        sim     CDS     211     211     .       -       .       ID=C_50;</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

212

</td>

<td class="new_line diff-line-num" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

212

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC212" class="line" lang="plaintext">gi|12345678|ref|NC_012345.1|        sim     CDS     212     212     .       -       .       ID=C_61;</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

213

</td>

<td class="new_line diff-line-num" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

213

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC213" class="line" lang="plaintext">gi|12345678|ref|NC_012345.1|        sim     CDS     213     213     .       -       .       ID=C_221;</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="314f9d77838daf9ce75df9af4e3e5cbae36dbaf9">

<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/50d748b5c10ee4ec1db1c0ec09e45d0f0dddb9cf#314f9d77838daf9ce75df9af4e3e5cbae36dbaf9"><strong>test/C2.faa</strong></a>

<hr>

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

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,4 +12,4 @@ AYRNIKKKGYDGGKAGTLVTLMEFVAQGRVANALFDWGSCNEEGAGLSKQCSETVVGFLQ</td>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

</td>

<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">QSSDYHRLFPKGYGEVPPRCTLGPFPAFHMLMQAALKGSFRTAQQPSVLFSCKCVKLKYS</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

</td>

<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">SCKYAL</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

</td>

<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">>C_11</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

</td>

<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA</span></pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA<span class="idiff left right">V</span></span></pre>

</td>

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