Dear all,<div><br></div><div>I&#39;m trying to set up samtools sort command on local Galaxy server.</div><div>But I can not success to get sorted files  from its result.</div><div><br></div><div>First time, I got error message from Galaxy as..</div>

<div>error at..</div><div>[bam_sort_core] merging from 13 files... </div><div>To resolve this problem, I use discard_stderr_wrapper.sh for modifying my samtools_sort.xml.</div><div>(<a href="http://wiki.galaxyproject.org/Future/Job%20Failure%20When%20stderr">http://wiki.galaxyproject.org/Future/Job%20Failure%20When%20stderr</a>)</div>

<div><div>in samtools_sort.xml############################################</div><div><div>&lt;command interpreter=&quot;sh&quot;&gt;</div><div><span class="Apple-tab-span" style="white-space:pre">	</span>discard_stderr_wrapper.sh samtools sort &#39;$input&#39; &#39;$output&#39;</div>

<div>&lt;/command&gt;</div></div><div>##################################################################</div><div><br></div><div>Then I can success to finish the samtools sort job.</div><div>But I can not get sorted file from Galaxy interface.</div>

<div>Sorted file exists in the results folder as &quot;dataset_97.dat.bam&quot;.  </div><div>But it could not link on Galaxy.</div><div>Do you have any suggestion for this problem?</div><div><br></div><div>thanks </div><div>

Masaki MS.</div>
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