Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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 ✭✭✭✭

    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.

Sign In or Register to comment.