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GATK GenotypeGVCFs: OutOfMemoryError: Java heap space

Hi GATK team,

I used the following commands to detect jointly variants. However, after trying many times, it always gave me the following errors even though I already set up JAVA "-Xms -Xmx" and temporary path like your suggestions in privous question. could you tell me how I solve this problem?

gatk-4.0.8.1/gatk --java-options "-Xms5g -Xmx64g" GenotypeGVCFs -R human_g1k_v37_decoy.fasta -V gendb:///home/zhuwenjuan/12/gendb -G StandardAnnotation -D dbsnp_138.b37.vcf.gz -O raw.12.vcf.gz -stand-call-conf 30.0 --TMP_DIR /home/zhuwenjuan/12/temp

Errors:
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at java.util.stream.StreamSupport.intStream(StreamSupport.java:138)
at java.util.Arrays.stream(Arrays.java:5053)
at java.util.Arrays.stream(Arrays.java:5035)
at org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.GeneralPloidyExactAFCalculator.isValidConformation(GeneralPloidyExactAFCalculator.java:315)
at org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.GeneralPloidyExactAFCalculator.computeLofK(GeneralPloidyExactAFCalculator.java:280)
at org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.GeneralPloidyExactAFCalculator.calculateACConformationAndUpdateQueue(GeneralPloidyExactAFCalculator.java:187)
at org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.GeneralPloidyExactAFCalculator.fastCombineMultiallelicPool(GeneralPloidyExactAFCalculator.java:148)
at org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.GeneralPloidyExactAFCalculator.combineSinglePools(GeneralPloidyExactAFCalculator.java:112)
at org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.GeneralPloidyExactAFCalculator.computeLog10PNonRef(GeneralPloidyExactAFCalculator.java:25)
at org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AFCalculator.getLog10PNonRef(AFCalculator.java:33)
at org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:255)
at org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:210)
at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs.calculateGenotypes(GenotypeGVCFs.java:266)
at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs.regenotypeVC(GenotypeGVCFs.java:222)
at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs.apply(GenotypeGVCFs.java:201)
at org.broadinstitute.hellbender.engine.VariantWalkerBase.lambda$traverse$0(VariantWalkerBase.java:151)
at org.broadinstitute.hellbender.engine.VariantWalkerBase$$Lambda$98/1374785073.accept(Unknown Source)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at org.broadinstitute.hellbender.engine.VariantWalkerBase.traverse(VariantWalkerBase.java:149)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137)

Answers

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