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.
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