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"GATK 4 ACNV Get Bayesian Hets Using Tumor and Normal for Capture" running out of memory

jjiaojjiao Member, Broadie

Some of my samples on Firehose running the task "GATK 4 ACNV Get Bayesian Hets Using Tumor and Normal for Capture" failed due to what seems like memory errors. An example error log is below:


Picked up JAVA_TOOL_OPTIONS: -Xmx1g -DR_HOME=/broad/software/free/Linux/redhat_6_x86_64/pkgs/r_2.10.1
[October 12, 2016 2:24:51 PM EDT] org.broadinstitute.hellbender.tools.exome.GetBayesianHetCoverage --reference /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta --normal /seq/picard_aggregation/RP-945/Exome/115WB_2-11-15/v2/115WB_2-11-15.bam --tumor /seq/picard_aggregation/RP-945/Exome/115A_3-18-14/v1/115A_3-18-14.bam --snpIntervals /xchip/tcga/Tools/gatk4cnv/allchr.1kg.phase3.v5a.snp.maf10.biallelic.recode.fixed.prune5.interval_list --normalHets 115T-TP-NB-SM-A2WOM-SM-A3PYW.normal.hets.tsv --tumorHets 115T-TP-NB-SM-A2WOM-SM-A3PYW.tumor.hets.tsv --readDepthThreshold 15 --minimumMappingQuality 30 --minimumBaseQuality 20 --hetCallingStringency 30.0 --minimumAbnormalFraction 0.8 --maximumAbnormalFraction 0.9 --maximumCopyNumber 2 --quadratureOrder 200 --errorAdjustmentFactor 1.0 --VALIDATION_STRINGENCY SILENT --help false --version false --verbosity INFO --QUIET false
[October 12, 2016 2:24:51 PM EDT] Executing as [email protected] on Linux 2.6.32-573.18.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_92-b14; Version: Version:version-unknown-SNAPSHOT
[October 12, 2016 9:27:09 PM EDT] org.broadinstitute.hellbender.tools.exome.GetBayesianHetCoverage done. Elapsed time: 422.31 minutes.
Runtime.totalMemory()=4275568640
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOf(Arrays.java:3181)
at java.util.ArrayList.grow(ArrayList.java:261)
at java.util.ArrayList.ensureExplicitCapacity(ArrayList.java:235)
at java.util.ArrayList.ensureCapacityInternal(ArrayList.java:227)
at java.util.ArrayList.addAll(ArrayList.java:579)
at htsjdk.samtools.BAMFileSpan.merge(BAMFileSpan.java:263)
at htsjdk.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:756)
at htsjdk.samtools.BAMFileReader.query(BAMFileReader.java:434)
at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:499)
at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:371)
at htsjdk.samtools.util.SamRecordIntervalIteratorFactory.makeSamRecordIntervalIterator(SamRecordIntervalIteratorFactory.java:76)
at htsjdk.samtools.util.SamLocusIterator.iterator(SamLocusIterator.java:222)
at org.broadinstitute.hellbender.tools.exome.pulldown.BayesianHetPulldownCalculator.getHetPulldown(BayesianHetPulldownCalculator.java:326)
at org.broadinstitute.hellbender.tools.exome.GetBayesianHetCoverage.runMatchedNormalTumor(GetBayesianHetCoverage.java:261)
at org.broadinstitute.hellbender.tools.exome.GetBayesianHetCoverage.doWork(GetBayesianHetCoverage.java:302)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:102)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:155)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:174)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:69)
at org.broadinstitute.hellbender.Main.main(Main.java:84)


"Reserved Disk Space" doesn't seem to be a field I can modify. Is there a task config somewhere where I can modify the amount of memory reserved for this task?

I looked at the task author and it says "gatkforums". Please let me know if I should be posting this elsewhere. Thanks!

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