java.lang.OutOfMemoryError: Requested array size exceeds VM limit

broadinstitute.org | 7 months ago
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Root Cause Analysis

  1. java.lang.OutOfMemoryError

    Requested array size exceeds VM limit

    at java.util.Arrays.copyOf()
  2. Java RT
    StringBuilder.append
    1. java.util.Arrays.copyOf(Arrays.java:2367)
    2. java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:130)
    3. java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:114)
    4. java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:415)
    5. java.lang.StringBuilder.append(StringBuilder.java:132)
    5 frames
  3. HTS JDK
    VCFWriter.add
    1. htsjdk.variant.vcf.VCFEncoder.addGenotypeData(VCFEncoder.java:342)
    2. htsjdk.variant.vcf.VCFEncoder.encode(VCFEncoder.java:145)
    3. htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:221)
    3 frames
  4. org.broadinstitute.gatk
    CommandLineGATK.main
    1. org.broadinstitute.gatk.engine.io.storage.VariantContextWriterStorage.add(VariantContextWriterStorage.java:182)
    2. org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub.add(VariantContextWriterStub.java:269)
    3. org.broadinstitute.gatk.tools.walkers.variantutils.CombineGVCFs.endPreviousStates(CombineGVCFs.java:269)
    4. org.broadinstitute.gatk.tools.walkers.variantutils.CombineGVCFs.reduce(CombineGVCFs.java:189)
    5. org.broadinstitute.gatk.tools.walkers.variantutils.CombineGVCFs.reduce(CombineGVCFs.java:110)
    6. org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociReduce.apply(TraverseLociNano.java:291)
    7. org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociReduce.apply(TraverseLociNano.java:280)
    8. org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:279)
    9. org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
    10. org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
    11. org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
    12. org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
    13. org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
    14. org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
    15. org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
    16. org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
    17. org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
    18. org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)
    18 frames