Hello,
I have been trying to resolve an issue that occurred in some of my samples while running GATK4 Haplotype Caller. After the program has been running for a while, it suddenly stops and this error pops up:
java.lang.IllegalStateException: Duplicate key [B@565e3f66
at java.util.stream.Collectors.lambda$throwingMerger$0(Collectors.java:133)
at java.util.HashMap.merge(HashMap.java:1253)
at java.util.stream.Collectors.lambda$toMap$58(Collectors.java:1320)
at java.util.stream.ReduceOps$3ReducingSink.accept(ReduceOps.java:169)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.buildGapContinuationPenalties(PairHMMLikelihoodCalculationEngine.java:304)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeReadLikelihoods(PairHMMLikelihoodCalculationEngine.java:253)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeReadLikelihoods(PairHMMLikelihoodCalculationEngine.java:187)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.callRegion(HaplotypeCallerEngine.java:520)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.apply(HaplotypeCaller.java:239)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:244)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:217)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:779)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:115)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:170)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:189)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:122)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:143)
at org.broadinstitute.hellbender.Main.main(Main.java:221)
I have tried removing duplicates using MarkDuplicates but this has not resolved the issue. I was wondering if others were having this issue and what could be causing it.
Thank you in advance for the help