Holiday Notice:
The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!

Latest Release: 02/05/19
Release Notes can be found here.

"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!

Tagged:

Answers

Sign In or Register to comment.