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<h1 class="quarto-secondary-nav-title"><span class="chapter-number">6</span> <span class="chapter-title">Options common to most of the <em>OBITools</em> commands</span></h1>
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<a href="./index.html" class="sidebar-item-text sidebar-link">Preface</a>
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<a href="./installation.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">1</span> <span class="chapter-title">Installation of the <em>OBITools</em></span></a>
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<a href="./formats.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">2</span> <span class="chapter-title">File formats usable with <em>OBITools</em></span></a>
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<a href="./tutorial.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">3</span> <span class="chapter-title">OBITools V4 Tutorial</span></a>
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<a href="./commands.html" class="sidebar-item-text sidebar-link">The *OBITools V4* commands</a>
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<a href="./inupt.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">4</span> <span class="chapter-title">Specifying the data input to <em>OBITools</em> commands</span></a>
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<a href="./output.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">5</span> <span class="chapter-title">Controling OBITools outputs</span></a>
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<a href="./common_options.html" class="sidebar-item-text sidebar-link active"><span class="chapter-number">6</span> <span class="chapter-title">Options common to most of the <em>OBITools</em> commands</span></a>
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<a href="./expressions.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">7</span> <span class="chapter-title">OBITools expression language</span></a>
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<a href="./comm_metabarcode_design.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">8</span> <span class="chapter-title">Metabarcode design and quality assessment</span></a>
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<a href="./comm_reformat.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">9</span> <span class="chapter-title">File format conversions</span></a>
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<a href="./comm_annotation.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span> <span class="chapter-title">Sequence annotations</span></a>
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<a href="./comm_computation.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">11</span> <span class="chapter-title">Computations on sequences</span></a>
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<a href="./comm_sampling.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">12</span> <span class="chapter-title">Sequence sampling and filtering</span></a>
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<a href="./comm_utilities.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">13</span> <span class="chapter-title">Utilities</span></a>
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<span class="sidebar-item-text sidebar-link text-start">The GO *OBITools* library</span>
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<a href="./annexes.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">A</span> <span class="chapter-title">Annexes</span></a>
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<a href="./references.html" class="sidebar-item-text sidebar-link">References</a>
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<h2 id="toc-title">Table of contents</h2>
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<ul>
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<li><a href="#helpful-options" id="toc-helpful-options" class="nav-link active" data-scroll-target="#helpful-options"><span class="toc-section-number">6.1</span> Helpful options</a></li>
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<li><a href="#system-related-options" id="toc-system-related-options" class="nav-link" data-scroll-target="#system-related-options"><span class="toc-section-number">6.2</span> System related options</a></li>
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<h1 class="title d-none d-lg-block"><span class="chapter-number">6</span> <span class="chapter-title">Options common to most of the <em>OBITools</em> commands</span></h1>
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<h2 data-number="6.1" class="anchored" data-anchor-id="helpful-options"><span class="header-section-number">6.1</span> Helpful options</h2>
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<dl>
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<dt><strong>--help</strong>, <strong>-h</strong></dt>
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<dd>
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<p>Display a friendly help message.</p>
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</dd>
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</dl>
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<p><strong>--no-progressbar</strong></p>
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</section>
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<section id="system-related-options" class="level2" data-number="6.2">
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<h2 data-number="6.2" class="anchored" data-anchor-id="system-related-options"><span class="header-section-number">6.2</span> System related options</h2>
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<p><strong>Managing parallel execution of tasks</strong></p>
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<p>A new feature of <em>OBITools</em> V4 is the ability to run multiple tasks in parallel, reading files, calculating on the data, formatting and writing the results. Each of these tasks can itself be parallelized by dividing the data into batches and running the calculation on several batches in parallel. This allows the overall calculation time of an <em>OBITools</em> command to be reduced considerably. The parameters organizing the parallel calculation are determined automatically to use the maximum capacity of your computer. But in some circumstances, it is necessary to override these default settings either to try to optimize the computation on a given machine, or to limit the OBITools to using only a part of the computational capacity. There are two options for doing this.</p>
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<dl>
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<dt><strong>--max-cpu</strong></dt>
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<dd>
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<p>OBITools V4 are able to run in parallel on all the CPU cores available on the computer. It is sometime required to limit the computation to a smaller number of cores. That option specify the maximum number of cores that the OBITools command can use. This behaviour can also be set up using the <code>OBIMAXCPU</code> environment variable.</p>
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</dd>
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</dl>
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<p><strong>--workers</strong>, <strong>-w</strong></p>
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<p>If your computer has 8 cores, but you want to limit <em>OBITools</em> to use only two of them you have several solution:</p>
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<ul>
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<li><p>If you want to set the limit for a single execution you can use the <strong>–max-cpu</strong> option</p>
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<div class="sourceCode" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obiconvert</span> <span class="at">--max-cpu</span> 2 <span class="at">--fasta-output</span> data.fastq <span class="op">></span> data.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<p>or you can precede the command by setting the environment variable <code>OBIMAXCPU</code></p>
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<div class="sourceCode" id="cb2"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="va">OBIMAXCPU</span><span class="op">=</span>2 <span class="ex">obiconvert</span> <span class="at">--fasta-output</span> data.fastq <span class="op">></span> data.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div></li>
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<li><p>If you want to set the limit to your complete session, you have to export <code>OBIMAXCPU</code></p>
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<div class="sourceCode" id="cb3"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="bu">export</span> <span class="va">OBIMAXCPU</span><span class="op">=</span>2 </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<p>all the following OBITools commands will be limited to use at max 2 CPU cores.</p></li>
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<li><p>If all the time you want to impose this limit, you must include the above <code>export</code> command in your <code>.bashrc</code> file.</p></li>
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</ul>
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<p><strong>OBITools debuging related options</strong></p>
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<p><strong>--debug</strong></p>
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<i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">5</span> <span class="chapter-title">Controling OBITools outputs</span></span>
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