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Samebug tips

  1. ,
    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.

  2. ,
    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 netbeans.org by Unknown author, 2 years ago
via GitHub by donghwan-shin
, 2 years 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 htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:221)	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)