I got the following rather strange error while running GATK indel realignment on a considerably larger file (HiSeq) than I am used to:
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.nio.HeapByteBuffer.<init>(HeapByteBuffer.java:39)
at java.nio.ByteBuffer.allocate(ByteBuffer.java:312)
at net.sf.picard.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:188)
at org.broadinstitute.sting.gatk.datasources.providers.ReferenceView.getReferenceBases(ReferenceView.java:89)
at org.broadinstitute.sting.gatk.datasources.providers.ReadReferenceView.getReferenceContext(ReadReferenceView.java:73)
at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(TraverseReads.java:87)
at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(TraverseReads.java:48)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:69)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:175)
at org.broadinstitute.sting.gatk.CommandLineExecutable.executeGATK(CommandLineExecutable.java:94)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:76)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:104)
which makes it look lik ...