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Adoni5 committed May 8, 2024
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<section id="frequently-asked-questions">
<h1>Frequently Asked Questions<a class="headerlink" href="#frequently-asked-questions" title="Link to this heading">#</a></h1>
<h1>Frequently Asked Questions<a class="headerlink" href="#frequently-asked-questions" title="Link to this heading"></a></h1>
<p><a name="connection-error-\[bad_reply\]-could-not-interpret-message-from-server-for-request:-load_config-reply:-invalid_protocol"></a></p>
<section id="connection-error-bad-reply-could-not-interpret-message-from-server-for-request-load-config-reply-invalid-protocol">
<h2>Connection error. [bad_reply] Could not interpret message from server for request: LOAD_CONFIG. Reply: INVALID_PROTOCOL<a class="headerlink" href="#connection-error-bad-reply-could-not-interpret-message-from-server-for-request-load-config-reply-invalid-protocol" title="Link to this heading">#</a></h2>
<h2>Connection error. [bad_reply] Could not interpret message from server for request: LOAD_CONFIG. Reply: INVALID_PROTOCOL<a class="headerlink" href="#connection-error-bad-reply-could-not-interpret-message-from-server-for-request-load-config-reply-invalid-protocol" title="Link to this heading"></a></h2>
<p>This is most likely a version mismatch between <code class="docutils literal notranslate"><span class="pre">ont-pyguppy-client-lib</span></code>, the python library that enables readfish to talk to Guppy and the installed version of Guppy.</p>
<p>If you open a terminal and run</p>
<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="go">guppy_basecall_server --version</span>
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<p><a name="connection-error-\[timed_out\]-timeout-waiting-for-reply-to-request:-load_config"></a></p>
</section>
<section id="connection-error-timed-out-timeout-waiting-for-reply-to-request-load-config">
<h2>Connection error. [timed_out] Timeout waiting for reply to request: LOAD_CONFIG<a class="headerlink" href="#connection-error-timed-out-timeout-waiting-for-reply-to-request-load-config" title="Link to this heading">#</a></h2>
<h2>Connection error. [timed_out] Timeout waiting for reply to request: LOAD_CONFIG<a class="headerlink" href="#connection-error-timed-out-timeout-waiting-for-reply-to-request-load-config" title="Link to this heading"></a></h2>
<p>This error often stems from a couple of sources. To test your Guppy Connection you can run</p>
<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="go">python -c &#39;from pyguppy_client_lib.pyclient import PyGuppyClient as PGC; \</span>
<span class="go"> c = PGC(&quot;ipc:///tmp/.guppy/5555&quot;, &quot;dna_r9.4.1_450bps_fast.cfg&quot;); \</span>
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<p><a name="how-do-i-create-a-readfish-python-environment"></a></p>
</section>
<section id="how-do-i-create-a-readfish-python-environment">
<h2>How do I create a readfish python environment?<a class="headerlink" href="#how-do-i-create-a-readfish-python-environment" title="Link to this heading">#</a></h2>
<h2>How do I create a readfish python environment?<a class="headerlink" href="#how-do-i-create-a-readfish-python-environment" title="Link to this heading"></a></h2>
<p>We recommend using conda to manage your readfish environments, especially on ONT machines!
To install conda instructions can be found <a class="reference external" href="https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html#regular-installation">here</a>.
An explanation is found in an answer to this <a class="reference external" href="https://github.com/LooseLab/readfish/issues/124#issuecomment-759599319">issue</a> as well.</p>
Expand Down Expand Up @@ -321,7 +384,7 @@ <h2>How do I create a readfish python environment?<a class="headerlink" href="#h
<p><a name="what-should-my-batch-times-look-like"></a></p>
</section>
<section id="what-should-my-batch-times-look-like">
<h2>What should my batch times look like.<a class="headerlink" href="#what-should-my-batch-times-look-like" title="Link to this heading">#</a></h2>
<h2>What should my batch times look like.<a class="headerlink" href="#what-should-my-batch-times-look-like" title="Link to this heading"></a></h2>
<p>When running readfish, you will see output scrolling down your terminal pane to the effect of</p>
<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="go">2023-01-17 19:18:57,355 ru.ru_gen 15R/0.50858s</span>
<span class="go">2023-01-17 19:18:57,834 ru.ru_gen 17R/0.47959s</span>
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<p><a name="which-branch-of-readfish-should-i-use"></a></p>
</section>
<section id="which-branch-of-readfish-should-i-use">
<h2>Which branch of readfish should I use?<a class="headerlink" href="#which-branch-of-readfish-should-i-use" title="Link to this heading">#</a></h2>
<h2>Which branch of readfish should I use?<a class="headerlink" href="#which-branch-of-readfish-should-i-use" title="Link to this heading"></a></h2>
<p>We are aware that readfish is a bit messy in terms of code branches right now (18/05/2023). Whilst we are working to bring this in to line, currently the most tried and tested version in <code class="docutils literal notranslate"><span class="pre">dev_staging</span></code>.
Watch this space for any updates!
See elsewhere in this file for installtion FAQs. 🕵️‍♂️</p>
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