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

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Samebug tips

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via oracle.com by Unknown author

An easy way to solve OutOfMemoryError in java is to increase the maximum heap size by using JVM options -Xmx512M, this will immediately solve your OutOfMemoryError.

,
via Stack Overflow by Eugene Yokota

In Eclipse : go to Run --> Run Configurations --> then select the project under maven build --> then select the tab "JRE" --> then enter -Xmx1024m

This should increase the memory heap for all the builds/projects. The above memory size is 1 GB

Solutions on the web

via broadinstitute.org by Unknown author, 1 year ago
Requested array size exceeds VM limit
via GitHub by zip62
, 1 year ago
GC overhead limit exceeded
via JFrog JIRA by Ariel Seftel, 1 year ago
Requested array size exceeds VM limit
via netbeans.org by Unknown author, 1 year ago
via GitHub by donghwan-shin
, 1 year ago
GC overhead limit exceeded
via Stack Overflow by dotwin
, 1 year ago
Requested array size exceeds VM limit
java.lang.OutOfMemoryError: Requested array size exceeds VM limit
at java.util.Arrays.copyOf(Arrays.java:2367)
at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:130)
at java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:114)
at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:415)
at java.lang.StringBuilder.append(StringBuilder.java:132)
at htsjdk.variant.vcf.VCFEncoder.addGenotypeData(VCFEncoder.java:342)
at htsjdk.variant.vcf.VCFEncoder.encode(VCFEncoder.java:145)
at org.broadinstitute.gatk.engine.io.storage.VariantContextWriterStorage.add(VariantContextWriterStorage.java:182)
at org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub.add(VariantContextWriterStub.java:269)
at org.broadinstitute.gatk.tools.walkers.variantutils.CombineGVCFs.endPreviousStates(CombineGVCFs.java:269)
at org.broadinstitute.gatk.tools.walkers.variantutils.CombineGVCFs.reduce(CombineGVCFs.java:189)
at org.broadinstitute.gatk.tools.walkers.variantutils.CombineGVCFs.reduce(CombineGVCFs.java:110)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociReduce.apply(TraverseLociNano.java:291)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociReduce.apply(TraverseLociNano.java:280)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:279)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)

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