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