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Unable to submit job

yahuiyahui chinaMember

Hi, Bob

I'm trying to use GenomeSTRiP to call CNV. While running CNV discovery with the command below:

java -Xmx4g -cp ${classpath} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-cp ${classpath} \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
-configFile ${SV_DIR}/conf/genstrip_parameters.txt \
-tempDir ${SV_TMPDIR} \
-R data/human_b36_chr1.fasta \
-genderMapFile data/installtest_gender.map \
-I ${bam} \
-md ${runDir}/metadata \
-runDirectory ${runDir} \
-jobLogDir ${runDir}/logs \
-tilingWindowSize 5000 \
-tilingWindowOverlap 2500 \
-maximumReferenceGapLength 2500 \
-boundaryPrecision 200 \
-minimumRefinedLength 2500 \
-jobRunner Drmaa \
-gatkJobRunner Drmaa \
-run \
|| exit 1

I ran into an error saying:

INFO 23:46:20,775 QScriptManager - Compiling 2 QScripts
INFO 23:46:41,701 QScriptManager - Compilation complete
INFO 23:46:41,859 HelpFormatter - ----------------------------------------------------------------------
INFO 23:46:41,859 HelpFormatter - Queue v3.3.GS2-0-g7ad6c61, Compiled 2015/10/04 09:18:40
INFO 23:46:41,859 HelpFormatter - Copyright (c) 2012 The Broad Institute
INFO 23:46:41,860 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 23:46:41,861 HelpFormatter - Program Args: -S /home/gaoyh/software/svtoolkit/qscript/discovery/cnv/CNVDiscoveryPipeline.q -S /home/gaoyh/software/svtoolkit/qscript/SVQScript.q -cp /home/gaoyh/software/svtoolkit/lib/SVToolkit.jar:/home/gaoyh/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/gaoyh/software/svtoolkit/lib/gatk/Queue.jar -gatk /home/gaoyh/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -configFile /home/gaoyh/software/svtoolkit/conf/genstrip_parameters.txt -tempDir ./tmpdir -R data/human_b36_chr1.fasta -genderMapFile data/installtest_gender.map -I data/installtest.bam -md test3/metadata -runDirectory test3 -jobLogDir test3/logs -tilingWindowSize 5000 -tilingWindowOverlap 2500 -maximumReferenceGapLength 2500 -boundaryPrecision 200 -minimumRefinedLength 2500 -jobRunner Drmaa -gatkJobRunner Drmaa -run
INFO 23:46:41,861 HelpFormatter - Executing as gaoyh@BigHeader on Linux 2.6.18-194.el5 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_51-b13.
INFO 23:46:41,862 HelpFormatter - Date/Time: 2016/01/14 23:46:41
INFO 23:46:41,862 HelpFormatter - ----------------------------------------------------------------------
INFO 23:46:41,863 HelpFormatter - ----------------------------------------------------------------------
INFO 23:46:41,878 QCommandLine - Scripting CNVDiscoveryPipeline
INFO 23:46:42,222 QCommandLine - Added 15 functions
INFO 23:46:42,222 QGraph - Generating graph.
INFO 23:46:42,256 QGraph - Running jobs.
INFO 23:46:42,623 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/gaoyh/software/svtoolkit/installtest/tmpdir' '-cp' '/home/gaoyh/software/svtoolkit/lib/SVToolkit.jar:/home/gaoyh/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/gaoyh/software/svtoolkit/lib/gatk/Queue.jar' '-cp' '/home/gaoyh/software/svtoolkit/lib/SVToolkit.jar:/home/gaoyh/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/gaoyh/software/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.gatk.queue.QCommandLine' '-cp' '/home/gaoyh/software/svtoolkit/lib/SVToolkit.jar:/home/gaoyh/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/gaoyh/software/svtoolkit/lib/gatk/Queue.jar' '-S' '/home/gaoyh/software/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStage1.q' '-S' '/home/gaoyh/software/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStageBase.q' '-S' '/home/gaoyh/software/svtoolkit/qscript/discovery/cnv/CNVDiscoveryGenotyper.q' '-S' '/home/gaoyh/software/svtoolkit/qscript/SVQScript.q' '-gatk' '/home/gaoyh/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar' '-jobLogDir' 'test3/cnv_stage1/seq_1/logs' '-memLimit' '2.0' '-jobRunner' 'Drmaa' '-gatkJobRunner' 'Drmaa' -run '-sequenceName' '1' '-runDirectory' 'test3/cnv_stage1/seq_1' '-sentinelFile' 'test3/cnv_sentinel_files/stage_1_seq_1.sent' --disableJobReport '-configFile' '/home/gaoyh/software/svtoolkit/conf/genstrip_parameters.txt' '-R' 'data/human_b36_chr1.fasta' '-ploidyMapFile' 'data/human_b36_chr1.ploidymap.txt' '-genomeMaskFile' 'data/human_b36_chr1.svmask.fasta' '-copyNumberMaskFile' 'data/human_b36_chr1.gcmask.fasta' '-readDepthMaskFile' 'data/human_b36_chr1.rdmask.bed' '-genderMapFile' 'data/installtest_gender.map' '-md' 'test3/metadata' -disableGATKTraversal '-I' 'test3/bam_headers/merged_headers.bam' '-intervalList' '1' '-scannedWindowsVcfFile' 'test3/cnv_stage1/seq_1/seq_1.sites.vcf.gz' '-tilingWindowSize' '5000' '-tilingWindowOverlap' '2500' '-maximumReferenceGapLength' '2500'
INFO 23:46:42,624 FunctionEdge - Output written to /home/gaoyh/software/svtoolkit/installtest/test3/logs/CNVDiscoveryPipeline-4.out
ERROR 23:46:42,668 Retry - Caught error during attempt 1 of 4.
org.broadinstitute.gatk.queue.QException: Unable to submit job: Bad UID for job execution: Bad UID for job execution MSG=ruserok failed validating gaoyh/gaoyh from BigHeader
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply$mcV$sp(DrmaaJobRunner.scala:89)
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply(DrmaaJobRunner.scala:85)
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply(DrmaaJobRunner.scala:85)
at org.broadinstitute.gatk.queue.util.Retry$.attempt(Retry.scala:49)
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner.start(DrmaaJobRunner.scala:85)
at org.broadinstitute.gatk.queue.engine.FunctionEdge.start(FunctionEdge.scala:84)
at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:434)
at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156)
at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
ERROR 23:46:42,672 Retry - Retrying in 1.0 minute.
ERROR 23:47:42,692 Retry - Caught error during attempt 2 of 4.
org.broadinstitute.gatk.queue.QException: Unable to submit job: Bad UID for job execution: Bad UID for job execution MSG=ruserok failed validating gaoyh/gaoyh from BigHeader
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply$mcV$sp(DrmaaJobRunner.scala:89)
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply(DrmaaJobRunner.scala:85)
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply(DrmaaJobRunner.scala:85)
at org.broadinstitute.gatk.queue.util.Retry$.attempt(Retry.scala:49)
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner.start(DrmaaJobRunner.scala:85)
at org.broadinstitute.gatk.queue.engine.FunctionEdge.start(FunctionEdge.scala:84)
at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:434)
at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156)
at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
ERROR 23:47:42,693 Retry - Retrying in 5.0 minutes.
ERROR 23:52:42,758 Retry - Caught error during attempt 3 of 4.
org.broadinstitute.gatk.queue.QException: Unable to submit job: Bad UID for job execution: Bad UID for job execution MSG=ruserok failed validating gaoyh/gaoyh from BigHeader
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply$mcV$sp(DrmaaJobRunner.scala:89)
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply(DrmaaJobRunner.scala:85)
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply(DrmaaJobRunner.scala:85)
at org.broadinstitute.gatk.queue.util.Retry$.attempt(Retry.scala:49)
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner.start(DrmaaJobRunner.scala:85)
at org.broadinstitute.gatk.queue.engine.FunctionEdge.start(FunctionEdge.scala:84)
at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:434)
at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156)
at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
ERROR 23:52:42,759 Retry - Retrying in 10.0 minutes.
ERROR 00:02:42,863 Retry - Caught error during attempt 4 of 4. Giving up.
org.broadinstitute.gatk.queue.QException: Unable to submit job: Bad UID for job execution: Bad UID for job execution MSG=ruserok failed validating gaoyh/gaoyh from BigHeader
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply$mcV$sp(DrmaaJobRunner.scala:89)
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply(DrmaaJobRunner.scala:85)
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply(DrmaaJobRunner.scala:85)
at org.broadinstitute.gatk.queue.util.Retry$.attempt(Retry.scala:49)
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner.start(DrmaaJobRunner.scala:85)
at org.broadinstitute.gatk.queue.engine.FunctionEdge.start(FunctionEdge.scala:84)
at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:434)
at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156)
at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
ERROR 00:02:42,883 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/gaoyh/software/svtoolkit/installtest/tmpdir' '-cp' '/home/gaoyh/software/svtoolkit/lib/SVToolkit.jar:/home/gaoyh/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/gaoyh/software/svtoolkit/lib/gatk/Queue.jar' '-cp' '/home/gaoyh/software/svtoolkit/lib/SVToolkit.jar:/home/gaoyh/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/gaoyh/software/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.gatk.queue.QCommandLine' '-cp' '/home/gaoyh/software/svtoolkit/lib/SVToolkit.jar:/home/gaoyh/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/gaoyh/software/svtoolkit/lib/gatk/Queue.jar' '-S' '/home/gaoyh/software/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStage1.q' '-S' '/home/gaoyh/software/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStageBase.q' '-S' '/home/gaoyh/software/svtoolkit/qscript/discovery/cnv/CNVDiscoveryGenotyper.q' '-S' '/home/gaoyh/software/svtoolkit/qscript/SVQScript.q' '-gatk' '/home/gaoyh/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar' '-jobLogDir' 'test3/cnv_stage1/seq_1/logs' '-memLimit' '2.0' '-jobRunner' 'Drmaa' '-gatkJobRunner' 'Drmaa' -run '-sequenceName' '1' '-runDirectory' 'test3/cnv_stage1/seq_1' '-sentinelFile' 'test3/cnv_sentinel_files/stage_1_seq_1.sent' --disableJobReport '-configFile' '/home/gaoyh/software/svtoolkit/conf/genstrip_parameters.txt' '-R' 'data/human_b36_chr1.fasta' '-ploidyMapFile' 'data/human_b36_chr1.ploidymap.txt' '-genomeMaskFile' 'data/human_b36_chr1.svmask.fasta' '-copyNumberMaskFile' 'data/human_b36_chr1.gcmask.fasta' '-readDepthMaskFile' 'data/human_b36_chr1.rdmask.bed' '-genderMapFile' 'data/installtest_gender.map' '-md' 'test3/metadata' -disableGATKTraversal '-I' 'test3/bam_headers/merged_headers.bam' '-intervalList' '1' '-scannedWindowsVcfFile' 'test3/cnv_stage1/seq_1/seq_1.sites.vcf.gz' '-tilingWindowSize' '5000' '-tilingWindowOverlap' '2500' '-maximumReferenceGapLength' '2500'
org.broadinstitute.gatk.queue.util.RetryException: Gave up after 4 attempts.
at org.broadinstitute.gatk.queue.util.Retry$.attempt(Retry.scala:63)
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner.start(DrmaaJobRunner.scala:85)
at org.broadinstitute.gatk.queue.engine.FunctionEdge.start(FunctionEdge.scala:84)
at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:434)
at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156)
at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
Caused by: org.broadinstitute.gatk.queue.QException: Unable to submit job: Bad UID for job execution: Bad UID for job execution MSG=ruserok failed validating gaoyh/gaoyh from BigHeader
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply$mcV$sp(DrmaaJobRunner.scala:89)
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply(DrmaaJobRunner.scala:85)
at org.broadinstitute.gatk.queue.engine.drmaa.DrmaaJobRunner$$anonfun$start$1.apply(DrmaaJobRunner.scala:85)
at org.broadinstitute.gatk.queue.util.Retry$.attempt(Retry.scala:49)
... 9 more
INFO 00:02:42,888 QGraph - 11 Pend, 1 Run, 0 Fail, 3 Done
INFO 00:02:42,895 QGraph - Writing incremental jobs reports...
INFO 00:02:42,896 QJobsReporter - Writing JobLogging GATKReport to file /home/gaoyh/software/svtoolkit/installtest/CNVDiscoveryPipeline.jobreport.txt
INFO 00:02:42,907 QGraph - 11 Pend, 0 Run, 1 Fail, 3 Done
INFO 00:02:42,910 QCommandLine - Writing final jobs report...
INFO 00:02:42,910 QJobsReporter - Writing JobLogging GATKReport to file /home/gaoyh/software/svtoolkit/installtest/CNVDiscoveryPipeline.jobreport.txt
INFO 00:02:42,911 QJobsReporter - Plotting JobLogging GATKReport to file /home/gaoyh/software/svtoolkit/installtest/CNVDiscoveryPipeline.jobreport.pdf
WARN 00:02:43,932 RScriptExecutor - RScript exited with 1. Run with -l DEBUG for more info.
INFO 00:02:43,935 QCommandLine - Done with errors
INFO 00:02:43,938 QGraph - -------
INFO 00:02:43,946 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/gaoyh/software/svtoolkit/installtest/tmpdir' '-cp' '/home/gaoyh/software/svtoolkit/lib/SVToolkit.jar:/home/gaoyh/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/gaoyh/software/svtoolkit/lib/gatk/Queue.jar' '-cp' '/home/gaoyh/software/svtoolkit/lib/SVToolkit.jar:/home/gaoyh/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/gaoyh/software/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.gatk.queue.QCommandLine' '-cp' '/home/gaoyh/software/svtoolkit/lib/SVToolkit.jar:/home/gaoyh/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/gaoyh/software/svtoolkit/lib/gatk/Queue.jar' '-S' '/home/gaoyh/software/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStage1.q' '-S' '/home/gaoyh/software/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStageBase.q' '-S' '/home/gaoyh/software/svtoolkit/qscript/discovery/cnv/CNVDiscoveryGenotyper.q' '-S' '/home/gaoyh/software/svtoolkit/qscript/SVQScript.q' '-gatk' '/home/gaoyh/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar' '-jobLogDir' 'test3/cnv_stage1/seq_1/logs' '-memLimit' '2.0' '-jobRunner' 'Drmaa' '-gatkJobRunner' 'Drmaa' -run '-sequenceName' '1' '-runDirectory' 'test3/cnv_stage1/seq_1' '-sentinelFile' 'test3/cnv_sentinel_files/stage_1_seq_1.sent' --disableJobReport '-configFile' '/home/gaoyh/software/svtoolkit/conf/genstrip_parameters.txt' '-R' 'data/human_b36_chr1.fasta' '-ploidyMapFile' 'data/human_b36_chr1.ploidymap.txt' '-genomeMaskFile' 'data/human_b36_chr1.svmask.fasta' '-copyNumberMaskFile' 'data/human_b36_chr1.gcmask.fasta' '-readDepthMaskFile' 'data/human_b36_chr1.rdmask.bed' '-genderMapFile' 'data/installtest_gender.map' '-md' 'test3/metadata' -disableGATKTraversal '-I' 'test3/bam_headers/merged_headers.bam' '-intervalList' '1' '-scannedWindowsVcfFile' 'test3/cnv_stage1/seq_1/seq_1.sites.vcf.gz' '-tilingWindowSize' '5000' '-tilingWindowOverlap' '2500' '-maximumReferenceGapLength' '2500'
INFO 00:02:43,946 QGraph - Log: /home/gaoyh/software/svtoolkit/installtest/test3/logs/CNVDiscoveryPipeline-4.out
INFO 00:02:43,948 QCommandLine - Script failed: 11 Pend, 0 Run, 1 Fail, 3 Done

and my workflow_manager is Torque/PBS.

So what should I do?

Thanks,
Yahui

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