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problem generating x.unfiltered.vcf

Will_GilksWill_Gilks University of Sussex, UKMember ✭✭

Hi,

I'm running GS/2.0 deletion detection and genotyping pipeline on 222 samples, 180Mb whole-genome Illumina, 30X coverage. Even after I've fixed all my other problems, I still get this java-out-of-memory error occurring mid-way through the 'identifying deletions' stage. The combined/final files for pairs, coverage, counts, coherence, and clusters are all full of data but the file x.unfiltered.vcf is empty. I'm not sure whether this is just a problem of computer memory, or whether there's something wrong with my input commands/variables. I've attached the whole log file. Any advice would be greatly appreciated,

William Gilks

End of log file from error:
INFO 00:46:36,456 DrmaaJobRunner - Submitted job id: 8063983 INFO 00:46:36,562 QGraph - 1 Pend, 1 Run, 0 Fail, 1870 Done ERROR 00:51:35,309 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/lustre/scratch/bioenv/wg39/LHm_analysis/genotyping/cnvs/tmpdir' '-cp' '/cm/shared/apps/svtoolkit/2.0.1602/lib/SVToolkit.jar:/cm/shared/apps/svtoolkit/2.0.1602/lib/gatk/GenomeAnalysisTK.jar:/cm/shared/apps/svtoolkit/2.0.1602/lib/gatk/Queue.jar' '-cp' '/cm/shared/apps/svtoolkit/2.0.1602/lib/SVToolkit.jar:/cm/shared/apps/svtoolkit/2.0.1602/lib/gatk/GenomeAnalysisTK.jar:/cm/shared/apps/svtoolkit/2.0.1602/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeDiscoveryOutput' '-O' '/lustre/scratch/bioenv/wg39/LHm_analysis/genotyping/cnvs/2016-02-17-10:41:51-lhm_rg_gstrip_small/lhm_rg_2016-03-08.small_dels.unfiltered.vcf' '-R' 'local_ref/dm6.fa' '-runDirectory' '2016-02-17-10:41:51-lhm_rg_gstrip_small' ERROR 00:51:35,316 FunctionEdge - Contents of /lustre/scratch/bioenv/wg39/LHm_analysis/genotyping/cnvs/2016-02-17-10:41:51-lhm_rg_gstrip_small/logs/SVDiscovery-1871.out: INFO 00:46:42,734 HelpFormatter - ------------------------------------------------------------- INFO 00:46:42,738 HelpFormatter - Program Name: org.broadinstitute.sv.apps.MergeDiscoveryOutput INFO 00:46:42,744 HelpFormatter - Program Args: -O /lustre/scratch/bioenv/wg39/LHm_analysis/genotyping/cnvs/2016-02-17-10:41:51-lhm_rg_gstrip_small/lhm_rg_2016-03-08.small_dels.unfiltered.vcf -R local_ref/dm6.fa -runDirectory 2016-02-17-10:41:51-lhm_rg_gstrip_small INFO 00:46:42,748 HelpFormatter - Executing as [email protected] on Linux 2.6.32-431.40.2.el6.nsc1.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_25-b15. INFO 00:46:42,749 HelpFormatter - Date/Time: 2016/02/18 00:46:42 INFO 00:46:42,750 HelpFormatter - ------------------------------------------------------------- INFO 00:46:42,751 HelpFormatter - ------------------------------------------------------------- Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at htsjdk.tribble.readers.PositionalBufferedStream.<init>(PositionalBufferedStream.java:47) at htsjdk.tribble.readers.PositionalBufferedStream.<init>(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.<init>(ParallelVCFIterator.java:53) at org.broadinstitute.sv.util.vcf.ParallelVCFIterator.<init>(ParallelVCFIterator.java:44) at org.broadinstitute.sv.common.RunFileMerger.mergeVCFFilesInternal(RunFileMerger.java:221) at org.broadinstitute.sv.common.RunFileMerger.mergeVCFOutputFiles(RunFileMerger.java:147) at org.broadinstitute.sv.discovery.SVDiscoveryMerger.mergePartitions(SVDiscoveryMerger.java:36) 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.MergeDiscoveryOutput.run(MergeDiscoveryOutput.java:59) 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.MergeDiscoveryOutput.main(MergeDiscoveryOutput.java:45) INFO 00:51:35,317 QGraph - Writing incremental jobs reports... INFO 00:51:35,317 QJobsReporter - Writing JobLogging GATKReport to file /lustre/scratch/bioenv/wg39/LHm_analysis/genotyping/cnvs/SVDiscovery.jobreport.txt INFO 00:51:36,282 QGraph - 1 Pend, 0 Run, 1 Fail, 1870 Done INFO 00:51:36,285 QCommandLine - Writing final jobs report... INFO 00:51:36,285 QJobsReporter - Writing JobLogging GATKReport to file /lustre/scratch/bioenv/wg39/LHm_analysis/genotyping/cnvs/SVDiscovery.jobreport.txt INFO 00:51:37,143 QJobsReporter - Plotting JobLogging GATKReport to file /lustre/scratch/bioenv/wg39/LHm_analysis/genotyping/cnvs/SVDiscovery.jobreport.pdf WARN 00:51:40,918 RScriptExecutor - RScript exited with 1. Run with -l DEBUG for more info. INFO 00:51:40,922 QCommandLine - Done with errors INFO 00:51:40,941 QGraph - ------- INFO 00:51:40,942 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/lustre/scratch/bioenv/wg39/LHm_analysis/genotyping/cnvs/tmpdir' '-cp' '/cm/shared/apps/svtoolkit/2.0.1602/lib/SVToolkit.jar:/cm/shared/apps/svtoolkit/2.0.1602/lib/gatk/GenomeAnalysisTK.jar:/cm/shared/apps/svtoolkit/2.0.1602/lib/gatk/Queue.jar' '-cp' '/cm/shared/apps/svtoolkit/2.0.1602/lib/SVToolkit.jar:/cm/shared/apps/svtoolkit/2.0.1602/lib/gatk/GenomeAnalysisTK.jar:/cm/shared/apps/svtoolkit/2.0.1602/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeDiscoveryOutput' '-O' '/lustre/scratch/bioenv/wg39/LHm_analysis/genotyping/cnvs/2016-02-17-10:41:51-lhm_rg_gstrip_small/lhm_rg_2016-03-08.small_dels.unfiltered.vcf' '-R' 'local_ref/dm6.fa' '-runDirectory' '2016-02-17-10:41:51-lhm_rg_gstrip_small' INFO 00:51:40,942 QGraph - Log: /lustre/scratch/bioenv/wg39/LHm_analysis/genotyping/cnvs/2016-02-17-10:41:51-lhm_rg_gstrip_small/logs/SVDiscovery-1871.out INFO 00:51:40,947 QCommandLine - Script failed: 1 Pend, 0 Run, 1 Fail, 1870 Done

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