Hi Nate,<div><br></div><div>I am running in daemon mode so this out of paster.log.</div><div><br></div><div>The job gets submitted to the PBS queue normally but the error shows up in history panel right away (also the working directory shows up during the cufflinks run):</div>


<div><br></div><div>
<a href="http://galaxy.jobs" target="_blank">galaxy.jobs</a> DEBUG 2011-10-24 17:51:25,567 dispatching job 595 to pbs runner</div><div><a href="http://galaxy.jobs" target="_blank">galaxy.jobs</a> INFO 2011-10-24 17:51:25,772 job 595 dispatched</div>


<div>
galaxy.jobs.runners.pbs DEBUG 2011-10-24 17:51:26,153 (595) submitting file /opt/hts_software/galaxy-parent/galaxy_server/galaxy-dist/database/pbs/595.sh</div><div>galaxy.jobs.runners.pbs DEBUG 2011-10-24 17:51:26,155 (595) command is: python /opt/hts_software/galaxy-parent/galaxy_server/galaxy-dist/tools/ngs_rna/cufflinks_wrapper.py              --input=/opt/hts_software/galaxy-parent/galaxy_server/galaxy-dist/database/files/001/dataset_1866.dat             --assembled-isoforms-output=/opt/hts_software/galaxy-parent/galaxy_server/galaxy-dist/database/files/002/dataset_2161.dat             --num-threads=&quot;6&quot;             -I 300000             -F 0.05             -j 0.05                                -g /opt/hts_software/galaxy-parent/galaxy_server/galaxy-dist/database/files/001/dataset_1699.dat                                        -b                     --ref_file=/opt/rnaseq_data/indices/bowtie/Salmonella/14028S/Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_14028S.fna                 --dbkey=14028S                  --index_dir=/opt/hts_software/galaxy-parent/galaxy_server/galaxy-dist/tool-data</div>



<div><div>galaxy.jobs.runners.pbs DEBUG 2011-10-24 17:51:26,157 (595) queued in batch queue as 303.localhost</div><div><a href="http://galaxy.jobs" target="_blank">galaxy.jobs</a> DEBUG 2011-10-24 17:51:26,599 dispatching job 596 to pbs runner</div>



<div><a href="http://galaxy.jobs" target="_blank">galaxy.jobs</a> INFO 2011-10-24 17:51:26,738 job 596 dispatchedgalaxy.jobs.runners.pbs DEBUG 2011-10-24 17:51:26,767 (595/303.localhost) PBS job state changed from N to R</div>


</div><div>
<br></div><div>Then later with no errors in paster.log when the cufflinks job is finishing (notice that it doesn&#39;t try to copy the contents of the working directory for this job like it normally does because galaxy thinks the job wasn&#39;t submitted to the queue even though it was):</div>


<div><br></div><div><div>galaxy.jobs.runners.pbs DEBUG 2011-10-24 19:05:57,402 (595/303.localhost) PBS job has left queue</div><div>galaxy.jobs.runners.pbs DEBUG 2011-10-24 19:05:57,402 (596/304.localhost) PBS job state changed from Q to R</div>


<div>galaxy.jobs.runners.pbs DEBUG 2011-10-24 21:29:01,995 (596/304.localhost) PBS job has left queue</div><div>galaxy.jobs.runners.pbs DEBUG 2011-10-24 21:29:01,995 (597/305.localhost) PBS job state changed from Q to R</div>


<div><a href="http://galaxy.jobs" target="_blank">galaxy.jobs</a> DEBUG 2011-10-24 21:29:02,999 finish(): Moved /opt/hts_software/galaxy-parent/galaxy_server/galaxy-dist/database/job_working_directory/596/isoforms.fpkm_tracking to /opt/hts_software/galaxy-parent/galaxy_server/galaxy-dist/database/files/002/dataset_2163.dat as directed by from_work_dir</div>


<div><a href="http://galaxy.jobs" target="_blank">galaxy.jobs</a> DEBUG 2011-10-24 21:29:03,555 finish(): Moved /opt/hts_software/galaxy-parent/galaxy_server/galaxy-dist/database/job_working_directory/596/genes.fpkm_tracking to /opt/hts_software/galaxy-parent/galaxy_server/galaxy-dist/database/files/002/dataset_2162.dat as directed by from_work_dir</div>


</div><div><br></div><div>Thanks,</div><div>Andrew</div><div><br><div class="gmail_quote">On Mon, Nov 7, 2011 at 4:00 PM, Nate Coraor <span dir="ltr">&lt;<a href="mailto:nate@bx.psu.edu" target="_blank">nate@bx.psu.edu</a>&gt;</span> wrote:<br>


<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>On Oct 25, 2011, at 2:43 AM, Andrew Warren wrote:<br>
<br>
&gt; Hello,<br>
&gt; I recently encountered a problem when trying to run Cufflinks on eight BAM files on our galaxy instance (via the multi-input toggle) and received the error: &quot;Unable to run job due to a misconfiguration of the Galaxy job running system&quot; for some, but not all, of the cufflinks jobs that appear in the history. These particular BAM files were copied over from the history of a larger workflow where they were successfully run through cufflinks. In the case of the problem workflow run, the cufflinks jobs are all successfully submitted to Torque PBS and continue to run and finish but many have this error displayed in the History. The jobs with the error displayed fail to copy files from the working directory to the database directory despite running to completion. We recently updated to galaxy-central changeset 6131:be6c89c33639. I have seen this error multiple times for this workflow, even after restarting galaxy. Does anyone have any ideas of what might be going wrong?<br>




<br>
</div>Hi Andrew,<br>
<br>
The error you&#39;re receiving indicates that there should also be a traceback logged to the Galaxy server log file or output when this occurs.  Could you check the log/output for such a traceback?<br>
<br>
Thanks,<br>
--nate<br>
<div><br>
&gt;<br>
&gt; Thanks for any help,<br>
&gt; Andrew Warren<br>
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