Running GenomeSTRiP to genotype results in Out of Memory Error

How is the java heap space increased in a queue script to run MergeGenotyperOutput ? I tried running the command with -Xmx6g parameter but the script ran with a heap space of only 2048m.

When running SVGenotyper I am getting the error below when running this command:
java -Xmx6g -cp ${classpath} ${mx} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/SVGenotyper.q \
-S ${SV_DIR}/qscript/SVQScript.q \
--disableJobReport \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
-cp ${classpath} \
-configFile ${SV_DIR}/conf/genstrip_parameters.txt \
-tempDir ${SV_TMPDIR} \
-R $REF \
-genderMapFile adsp_gender.map \
-runDirectory ${runDir} \
-md run.washu/metadata \
-md run.bcm/metadata \
-md run.bi/metadata \
-disableGATKTraversal \
-jobLogDir ${runDir}/logs \
-I ${bam} \
-vcf ${sites} \
-O ${genotypes} \
-jobRunner GridEngine\
-parallelRecords 100\
-run \
|| exit 1

INFO 00:10:21,266 RunFileMerger - Merging .genotypes.srinfo.dat files ...
INFO 00:10:21,267 RunFileMerger - INFILE run.scalpel.wgs.20bp/P0001.genotypes.srinfo.dat
INFO 00:40:33,841 RunFileMerger - Merging .genotypes.map.dat files ...
INFO 00:40:33,846 RunFileMerger - INFILE run.scalpel.wgs.20bp/P0001.genotypes.map.dat
INFO 00:40:59,453 RunFileMerger - INFILE run.scalpel.wgs.20bp/P0001.genotypes.vcf.gz
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at htsjdk.tribble.readers.PositionalBufferedStream.(PositionalBufferedStream.java:47)
at htsjdk.tribble.readers.PositionalBufferedStream.(PositionalBufferedStream.java:42)
at htsjdk.tribble.TabixFeatureReader.iterator(TabixFeatureReader.java:129)
at org.broadinstitute.sv.util.vcf.VCFReader.iterator(VCFReader.java:69)
at org.broadinstitute.sv.util.vcf.ParallelVCFIterator.makeIterator(ParallelVCFIterator.java:103)
at org.broadinstitute.sv.util.vcf.ParallelVCFIterator.(ParallelVCFIterator.java:53)
at org.broadinstitute.sv.util.vcf.ParallelVCFIterator.(ParallelVCFIterator.java:44)
at org.broadinstitute.sv.common.RunFileMerger.mergeVCFFilesInternal(RunFileMerger.java:222)
at org.broadinstitute.sv.common.RunFileMerger.mergeVCFOutputFiles(RunFileMerger.java:147)
at org.broadinstitute.sv.genotyping.SVGenotyperMerger.mergePartitions(SVGenotyperMerger.java:41)
at org.broadinstitute.sv.common.RunFileMerger.merge(RunFileMerger.java:93)
at org.broadinstitute.sv.common.RunFileMerger.merge(RunFileMerger.java:83)
at org.broadinstitute.sv.apps.MergeGenotyperOutput.run(MergeGenotyperOutput.java:54)
at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:54)
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.sv.commandline.CommandLineProgram.runAndReturnResult(CommandLineProgram.java:29)
at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
at org.broadinstitute.sv.apps.MergeGenotyperOutput.main(MergeGenotyperOutput.java:43)
INFO 00:42:28,659 QGraph - Writing incremental jobs reports...
INFO 00:42:28,728 QGraph - 0 Pend, 0 Run, 1 Fail, 1237 Done
INFO 00:42:28,738 QCommandLine - Writing final jobs report...
INFO 00:42:28,740 QCommandLine - Done with errors
INFO 00:42:28,751 QGraph - -------
INFO 00:42:28,752 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/restricted/projectnb/casa/sv/gs/tmpdir' '-cp' '/restricted/projectnb/casa/sv/gs/svtoolkit/lib/SVToolkit.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/Queue.jar' '-cp' '/restricted/projectnb/casa/sv/gs/svtoolkit/lib/SVToolkit.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeGenotyperOutput' '-O' '/restricted/projectnb/casa/sv/gs/adsp.sv.wgs.scalpel.noma.pass.del.gs.ge20bp.vcf' '-R' '/restricted/projectnb/casa/sv/gs/svtoolkit/1000G_phase1/human_g1k_v37.fasta' '-runDirectory' 'run.scalpel.wgs.20bp'
INFO 00:42:28,753 QGraph - Log: /restricted/projectnb/casa/sv/gs/run.scalpel.wgs.20bp/logs/SVGenotyper-1238.out
INFO 00:42:28,755 QCommandLine - Script failed: 0 Pend, 0 Run, 1 Fail, 1237 Done

Best Answer

Answers

  • shleeshlee CambridgeMember, Broadie, Moderator

    Hi @jfarrell,

    I let someone from the GenomeStrip team know a few days ago that you are asking a question. I hope they get back to you soon. It's possible we'll have to wait until next year, after the holidays, for an answer. If you're unable to resolve this issue in the meanwhile, be sure to post a comment within this thread to bring this issue to our attention.

    Happy holidays.

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