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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/ampliconnoise">Debian Med / ampliconnoise</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ampliconnoise/-/commit/bd6bbbed3115f8668fca27bfbc7ca9fd19d77f28">bd6bbbed</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-08-08T18:21:24+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Try --use-hwthread-cpus in openmpi for autopkgtest
</pre>
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<h4>1 changed file:</h4>
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<li class="file-stats">
<a href="#9e0a41fea6bf07d2509098822a219f1560531619">
debian/tests/Run.sh
</a>
</li>
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<h4>Changes:</h4>
<li id="9e0a41fea6bf07d2509098822a219f1560531619">
<a href="https://salsa.debian.org/med-team/ampliconnoise/-/commit/bd6bbbed3115f8668fca27bfbc7ca9fd19d77f28#9e0a41fea6bf07d2509098822a219f1560531619"><strong>debian/tests/Run.sh</strong></a>
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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">@@ -2,7 +2,7 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">nodes</span><span class="o" style="font-weight: 600;">=</span><span class="idiff left right">4</span> <span class="c" style="color: #998; font-style: italic;">#no. of cluster nodes to use</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">nodes</span><span class="o" style="font-weight: 600;">=</span><span class="idiff left right">2</span> <span class="c" style="color: #998; font-style: italic;">#no. of cluster nodes to use</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">file</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="c" style="color: #998; font-style: italic;">#first argument name of dat file</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="nv" style="color: #008080;">defaultPrimer</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"ATTAGATACCC[ACTG]GGTAG"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,7 +13,7 @@ stub=${file%.dat}</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Calculating .fdist file"</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell">mpirun <span class="nv" style="color: #008080;">$mpiextra</span> <span class="nt" style="color: #000080;">-<span class="idiff left">np</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$node</span>s</span> PyroDist <span class="nt" style="color: #000080;">-in</span> <span class="nv" style="color: #008080;">$file</span> <span class="nt" style="color: #000080;">-out</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>.fout</span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">mpirun <span class="nv" style="color: #008080;">$mpiextra</span> <span class="nt" style="color: #000080;">-<span class="idiff left right">-use-hwthread-cpu</span>s</span> PyroDist <span class="nt" style="color: #000080;">-in</span> <span class="nv" style="color: #008080;">$file</span> <span class="nt" style="color: #000080;">-out</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>.fout</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Clustering .fdist file"</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="23" style="width: 35px; color: rgba(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="23" style="width: 35px; color: rgba(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">@@ -23,24 +23,24 @@ rm ${stub}.fdist</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_X.otu <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_X.tree</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Running PyroNoise"</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell">mpirun <span class="nv" style="color: #008080;">$mpiextra</span> <span class="nt" style="color: #000080;">-<span class="idiff left">np</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$node</span>s</span> PyroNoiseM <span class="nt" style="color: #000080;">-din</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">file</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: #000080;">-out</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01 <span class="nt" style="color: #000080;">-lin</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_X.list <span class="nt" style="color: #000080;">-s</span> 60.0 <span class="nt" style="color: #000080;">-c</span> 0.01 <span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01.pout</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell">mpirun <span class="nv" style="color: #008080;">$mpiextra</span> <span class="nt" style="color: #000080;">-<span class="idiff left right">-use-hwthread-cpu</span>s</span> PyroNoiseM <span class="nt" style="color: #000080;">-din</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">file</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: #000080;">-out</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01 <span class="nt" style="color: #000080;">-lin</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_X.list <span class="nt" style="color: #000080;">-s</span> 60.0 <span class="nt" style="color: #000080;">-c</span> 0.01 <span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01.pout</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell">/usr/share/ampliconnoise/Scripts/Truncate.pl 220 < <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_cd.fa <span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220.fa</span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Running SeqDist"</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell">mpirun <span class="nv" style="color: #008080;">$mpiextra</span> <span class="nt" style="color: #000080;">-<span class="idiff left">np</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$node</span>s</span> SeqDist <span class="nt" style="color: #000080;">-in</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220.fa <span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220.seqdist</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell">mpirun <span class="nv" style="color: #008080;">$mpiextra</span> <span class="nt" style="color: #000080;">-<span class="idiff left right">-use-hwthread-cpu</span>s</span> SeqDist <span class="nt" style="color: #000080;">-in</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220.fa <span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220.seqdist</span>
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32
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"></span>
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell">FCluster <span class="nt" style="color: #000080;">-in</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220.seqdist <span class="nt" style="color: #000080;">-out</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220_S <span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220.fcout</span>
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34
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="shell"></span>
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35
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Running SeqNoise"</span></span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="shell">mpirun <span class="nv" style="color: #008080;">$mpiextra</span> <span class="nt" style="color: #000080;">-<span class="idiff left">np</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$node</span>s</span> SeqNoise <span class="nt" style="color: #000080;">-in</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220.fa <span class="nt" style="color: #000080;">-din</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220.seqdist <span class="nt" style="color: #000080;">-lin</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220_S.list <span class="nt" style="color: #000080;">-out</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220_s30_c08 <span class="nt" style="color: #000080;">-s</span> 30.0 <span class="nt" style="color: #000080;">-c</span> 0.08 <span class="nt" style="color: #000080;">-min</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01.mapping <span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220.snout</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell">mpirun <span class="nv" style="color: #008080;">$mpiextra</span> <span class="nt" style="color: #000080;">-<span class="idiff left right">-use-hwthread-cpu</span>s</span> SeqNoise <span class="nt" style="color: #000080;">-in</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220.fa <span class="nt" style="color: #000080;">-din</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220.seqdist <span class="nt" style="color: #000080;">-lin</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220_S.list <span class="nt" style="color: #000080;">-out</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220_s30_c08 <span class="nt" style="color: #000080;">-s</span> 30.0 <span class="nt" style="color: #000080;">-c</span> 0.08 <span class="nt" style="color: #000080;">-min</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01.mapping <span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220.snout</span>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="shell"></span>
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38
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220_S.otu <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220_S.tree <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220.seqdist</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Remove degenerate primers"</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^${primer}//'</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220_s30_c08_cd.fa <span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220_s30_c08_P.fa</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Clustering OTUs"</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="shell">mpirun <span class="nv" style="color: #008080;">$mpiextra</span> <span class="nt" style="color: #000080;">-<span class="idiff left">np</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$node</span>s</span> NDist <span class="nt" style="color: #000080;">-i</span> <span class="nt" style="color: #000080;">-in</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220_s30_c08_P.fa <span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220_s30_c08_P.ndist</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell">mpirun <span class="nv" style="color: #008080;">$mpiextra</span> <span class="nt" style="color: #000080;">-<span class="idiff left right">-use-hwthread-cpu</span>s</span> NDist <span class="nt" style="color: #000080;">-i</span> <span class="nt" style="color: #000080;">-in</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220_s30_c08_P.fa <span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220_s30_c08_P.ndist</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"> </span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="shell">FCluster <span class="nt" style="color: #000080;">-i</span> <span class="nt" style="color: #000080;">-in</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220_s30_c08_P.ndist <span class="nt" style="color: #000080;">-out</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220_s30_c08_P <span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">stub</span><span class="k" style="font-weight: 600;">}</span>_s60_c01_T220_s30_c08_P.fcout</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell"></span>
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