https://dev.arvados.org/https://dev.arvados.org/favicon.ico?15576888422020-10-28T14:44:42ZArvadosArvados - Idea #17049: Make a single chromosome run of the demohttps://dev.arvados.org/issues/17049?journal_id=883052020-10-28T14:44:42ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Related to</strong> <i><a class="issue tracker-6 status-1 priority-4 priority-default" href="/issues/17001">Idea #17001</a>: Arvados uses WB2 by default</i> added</li></ul> Arvados - Idea #17049: Make a single chromosome run of the demohttps://dev.arvados.org/issues/17049?journal_id=885612020-11-05T20:50:27ZJiayong Lijli@curii.com
<ul><li><strong>Tracker</strong> changed from <i>Bug</i> to <i>Idea</i></li></ul> Arvados - Idea #17049: Make a single chromosome run of the demohttps://dev.arvados.org/issues/17049?journal_id=891682020-12-01T22:03:40ZJiayong Lijli@curii.com
<ul><li><strong>Description</strong> updated (<a title="View differences" href="/journals/89168/diff?detail_id=85905">diff</a>)</li></ul> Arvados - Idea #17049: Make a single chromosome run of the demohttps://dev.arvados.org/issues/17049?journal_id=894482020-12-15T22:29:16ZJiayong Lijli@curii.com
<ul><li><strong>Status</strong> changed from <i>New</i> to <i>Feedback</i></li><li><strong>Description</strong> updated (<a title="View differences" href="/journals/89448/diff?detail_id=86167">diff</a>)</li></ul><p>branch 17049-make-singlechrom, commit d2f6d47da38e96de4597bb58ba1193e261af8fb1</p>
<p>I finished a run for chr19 input fastqs for 5 samples.<br /><a class="external" href="https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-3dqeqodgi1usk0r">https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-3dqeqodgi1usk0r</a></p>
<p>I encountered a gatk bug that the memory usage spikes when writing result vcf in the haplotypecaller step, if the region is outside of chr19. (And in general, in regions when very few reads are placed.) I had to schedule 14G ram machines for that step to complete it. (See failure <a class="external" href="https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-v0sq9csiz1p94nx">https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-v0sq9csiz1p94nx</a>)</p>
<p>Also I had to upload a different docker image for curii/clinvar-report to keep in order to finish the gvcf-to-vcf step (see failure <a class="external" href="https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-zulp4y3e9f7tv59">https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-zulp4y3e9f7tv59</a>). The new docker image is <a class="external" href="https://workbench.su92l.arvadosapi.com/collections/su92l-4zz18-kl40n4746vmjnw2">https://workbench.su92l.arvadosapi.com/collections/su92l-4zz18-kl40n4746vmjnw2</a></p>
<p>Input fastqs here <a class="external" href="https://workbench.su92l.arvadosapi.com/collections/su92l-4zz18-j1jotbx4uqckkec">https://workbench.su92l.arvadosapi.com/collections/su92l-4zz18-j1jotbx4uqckkec</a><br />The run for generating the chr19 input fastqs is <a class="external" href="https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-ilo79fgj728afkl">https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-ilo79fgj728afkl</a></p> Arvados - Idea #17049: Make a single chromosome run of the demohttps://dev.arvados.org/issues/17049?journal_id=894542020-12-16T15:05:00ZPeter Amstutzpeter.amstutz@curii.com
<ul></ul><p>So the goal of this was to have a relatively lightweight pipeline that still had all the pieces of the whole genome pipeline.</p>
<p>I think this still needs a little work to be lightweight --</p>
<p>I see dozens of haplotype caller instances that are each running for 1-2 minutes. Can we consolidate that?</p>
<p>Same for selectvariants/basecalibrator/applyBSQR. Can we either (a) not scatter or (b) use the <a href="https://doc.arvados.org/v2.1/user/cwl/cwl-extensions.html#RunInSingleContainer" class="external">RunInSingleContainer</a> feature.</p> Arvados - Idea #17049: Make a single chromosome run of the demohttps://dev.arvados.org/issues/17049?journal_id=895272020-12-28T22:11:46ZJiayong Lijli@curii.com
<ul></ul><p>branch 17049-make-singlechrom, commit d2f6d47da38e96de4597bb58ba1193e261af8fb1</p>
<p>I changed the fullintervallist to reflect chr19 only calling, hopefully this run is better.<br /><a class="external" href="https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-1l4x28f6q1rn955">https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-1l4x28f6q1rn955</a></p> Arvados - Idea #17049: Make a single chromosome run of the demohttps://dev.arvados.org/issues/17049?journal_id=899132021-01-14T22:50:41ZJiayong Lijli@curii.com
<ul><li><strong>Status</strong> changed from <i>Feedback</i> to <i>Resolved</i></li></ul><p>commit d147d1d1fafeeea06bd09d9479337b0f5aab43b0</p>
<p>Added comments for the singe chrom chr19 yml.</p>