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Not to generate final svdiscovery.dels.vcf

SyedSyed IndiaMember

Hi All,

I was running
java -Xmx16g -cp ${classpath} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/SVDiscovery.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-cp ${classpath} \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
-configFile ${SV_DIR}/conf/genstrip_parameters.txt \
-R /gpfs/projects/ref_data/reference/Homo_sapiens/ncbi/hs37d5/hs37d5.fa \
-I ../../CMT-5_S1_L001.sorted.bam \
-genderMapFile testInputs/gendarMap.txt \
-md output_metadata_directory \
-runDirectory run1_SVDiscovery \
-jobLogDir run1_SVDiscovery/logs \
-O run1_SVDiscovery/svdiscovery.dels.vcf \
-minimumSize 100 \
-maximumSize 100000 \
-run

and I was able to generate files like P0001.discovery.vcf.gz upto P0086.discovery.vcf.gz in this folder run1_SVDiscovery but didn't able to get final output file. Can some one let me know what would be the possible issue ?

Below is last few lines of logs file and I am not sure about any possible reason for not getting final SVDiscovery files.

INFO 02:23:55,691 QGraph - Writing incremental jobs reports...
INFO 02:23:55,691 QJobsReporter - Writing JobLogging GATKReport to file /gpfs/projects/bioinfo/najeeb/cnvPipeline/svtoolkit_2.00.1696/svtoolkit/SVDiscovery.jobreport.txt
INFO 02:23:55,803 QGraph - 2 Pend, 0 Run, 1 Fail, 85 Done
INFO 02:23:55,805 QCommandLine - Writing final jobs report...
INFO 02:23:55,805 QJobsReporter - Writing JobLogging GATKReport to file /gpfs/projects/bioinfo/najeeb/cnvPipeline/svtoolkit_2.00.1696/svtoolkit/SVDiscovery.jobreport.txt
INFO 02:23:55,852 QJobsReporter - Plotting JobLogging GATKReport to file /gpfs/projects/bioinfo/najeeb/cnvPipeline/svtoolkit_2.00.1696/svtoolkit/SVDiscovery.jobreport.pdf
WARN 02:23:59,178 RScriptExecutor - RScript exited with 1. Run with -l DEBUG for more info.
INFO 02:23:59,183 QCommandLine - Done with errors
INFO 02:23:59,189 QGraph - -------
INFO 02:23:59,195 QGraph - Failed: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/gpfs/projects/bioinfo/najeeb/cnvPipeline/svtoolkit_2.00.1696/svtoolkit/.queue/tmp' '-cp' '/gpfs/projects/bioinfo/najeeb/cnvPipeline/svtoolkit_2.00.1696/svtoolkit/lib/SVToolkit.jar:/gpfs/projects/bioinfo/najeeb/cnvPipeline/svtoolkit_2.00.1696/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/gpfs/projects/bioinfo/najeeb/cnvPipeline/svtoolkit_2.00.1696/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '/gpfs/projects/ref_data/reference/Homo_sapiens/ncbi/hs37d5/hs37d5.fa' '-I' '../../CMT-5_S1_L001.sorted.bam' '-O' '/gpfs/projects/bioinfo/najeeb/cnvPipeline/svtoolkit_2.00.1696/svtoolkit/run1_SVDiscovery/P0053.discovery.vcf.gz' '-disableGATKTraversal' 'true' '-md' 'output_metadata_directory' '-configFile' '/gpfs/projects/bioinfo/najeeb/cnvPipeline/svtoolkit_2.00.1696/svtoolkit/conf/genstrip_parameters.txt' '-runDirectory' 'run1_SVDiscovery' '-genderMapFile' 'testInputs/gendarMap.txt' '-partitionName' 'P0053' '-runFilePrefix' 'P0053' -L GL000230.1:1-43691 -searchLocus GL000230.1:1-43691 -searchWindow GL000230.1:1-43691 -searchMinimumSize 100 -searchMaximumSize 100000
INFO 02:23:59,196 QGraph - Log: /gpfs/projects/bioinfo/najeeb/cnvPipeline/svtoolkit_2.00.1696/svtoolkit/run1_SVDiscovery/logs/SVDiscovery-53.out
INFO 02:23:59,199 QCommandLine - Script failed: 2 Pend, 0 Run, 1 Fail, 85 Done

Thanks
Syed

Answers

  • bhandsakerbhandsaker Member, Broadie, Moderator admin

    You need to look in the log file for the job that failed:
    /gpfs/projects/bioinfo/najeeb/cnvPipeline/svtoolkit_2.00.1696/svtoolkit/run1_SVDiscovery/logs/SVDiscovery-53.out
    If it appears to be a transient error (disk full, random I/O error) you can rerun the top level script which will just retry the failed job.

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