>
> On Jan 5, 2012, at 11:46 AM, Ryan Golhar wrote:
>
> > I have three bam files that I'm trying to merge.  The job runs for a bit
> then errors saying there is a problem.  When I look at runner0.log I see:
> >
> > galaxy.jobs.runners.pbs DEBUG 2012-01-05 00:12:50,193 (19) submitting
> file /home/galaxy/galaxy-dist-9/database/pbs/19.sh
> > galaxy.jobs.runners.pbs DEBUG 2012-01-05 00:12:50,193 (19) command is:
> java -Xmx2G -jar
> /home/galaxy/galaxy-dist-9/tool-data/shared/jars/picard/MergeSamFiles.jar
> MSD=true VALIDATION_STRINGENCY=LENIENT
> O=/home/galaxy/galaxy-dist-9/database/files/000/dataset_96.dat
> I=/mnt/isilon/cag/ngs/hiseq/golharr/FALK05/solid5500_2_Falk05_JMF3_5_20111024_1_04-1-Idx_1-1.bam
> I=/mnt/isilon/cag/ngs/hiseq/golharr/FALK05/solid5500_2_Falk05_JMF3_5_20111024_1_05-2-Idx_1-1.bam
>
>  
> I=/mnt/isilon/cag/ngs/hiseq/golharr/FALK05/solid5500_2_Falk05_JMF3_5_20111024_1_06-3-Idx_1-1.bam
>     2> /home/galaxy/galaxy-dist-9/database/files/000/dataset_97.dat     ||
> echo "Error running Picard MergeSamFiles" >&2; cd
> /home/galaxy/galaxy-dist-9; /home/galaxy/galaxy-dist-9/set_metadata.sh
> ./database/files ./database/tmp . datatypes_conf.xml
> ./database/job_working_directory/19/galaxy.json
> database/tmp/metadata_in_HistoryDatasetAssociation_16_MuM7TP,database/tmp/metadata_kwds_HistoryDatasetAssociation_16_7w3ZvM,database/tmp/metadata_out_HistoryDatasetAssociation_16_m9A_X4,database/tmp/metadata_results_HistoryDatasetAssociation_16_cRV8Uj,,database/tmp/metadata_override_HistoryDatasetAssociation_16_5n8tqL
> database/tmp/metadata_in_HistoryDatasetAssociation_15_SUEdLf,database/tmp/metadata_kwds_HistoryDatasetAssociation_15_nt8MTH,database/tmp/metadata_out_HistoryDatasetAssociation_15_EEIJ_o,database/tmp/metadata_results_HistoryDatasetAssociation_15_7PhiXX,,database/tmp/metadata_override_HistoryDatasetAssociation_15_e_bdeW
> > galaxy.jobs.runners.pbs DEBUG 2012-01-05 00:12:50,206 (19) queued in
> default queue as 29.localhost.localdomain
> > galaxy.jobs.runners.pbs DEBUG 2012-01-05 00:12:50,253
> (19/29.localhost.localdomain) PBS job state changed from N to R
> > galaxy.jobs.runners.pbs DEBUG 2012-01-05 01:13:28,111
> (19/29.localhost.localdomain) PBS job state changed from R to C
> > galaxy.jobs.runners.pbs ERROR 2012-01-05 01:13:28,111
> (19/29.localhost.localdomain) PBS job failed: Unknown error: -10
> > galaxy.datatypes.metadata DEBUG 2012-01-05 01:13:28,272 Cleaning up
> external metadata files
> > galaxy.datatypes.metadata DEBUG 2012-01-05 01:13:28,286 Failed to
> cleanup MetadataTempFile temp files from
> database/tmp/metadata_out_HistoryDatasetAssociation_15_EEIJ_o: No JSON
> object could be decoded: line 1 column 0 (char 0)
> > galaxy.datatypes.metadata DEBUG 2012-01-05 01:13:28,286 Failed to
> cleanup MetadataTempFile temp files from
> database/tmp/metadata_out_HistoryDatasetAssociation_16_m9A_X4: No JSON
> object could be decoded: line 1 column 0 (char 0)
> >
> >
> > It looks like the job failed with "PBS job failed: Unknown error: -10".
>  Is there a way to set up Galaxy to keep job submission files?  I thought
> there was but don't see the option in universe_wsgi.ini for this.
>
> Hrm, there's no PBS exit code for -10:
>
>    http://www.clusterresources.com/torquedocs/2.7jobexitstatus.shtml
>
> In recent versions, the setting in the Galaxy config to keep job files is:
>
>    cleanup_job = never
>

I discovered the problem.  My pbs queue has a wall time restriction of 3600
seconds.

Is there a way to configure Galaxy to keep the job files for only failed
jobs?  I'd like to keep these two settings on, but find it unnecessary if
jobs successfully complete.
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