To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits
LATEST RELEASE: FireCloud's latest release was on February 13th. Release Notes can be found here.

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

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 cgaadm@node1532.broadinstitute.org 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.