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java.lang.IndexOutOfBoundsException: Index: 28, Size: 6 at java.util.LinkedList.checkElementIndex(Unknown Source) at java.util.LinkedList.get(Unknown Source) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.DanglingChainMergingGraph.mergeDanglingTail(DanglingChainMergingGraph.java:272) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.DanglingChainMergingGraph.recoverDanglingTail(DanglingChainMergingGraph.java:184) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.DanglingChainMergingGraph.recoverDanglingTails(DanglingChainMergingGraph.java:131) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler.createGraph(ReadThreadingAssembler.java:202) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler.assemble(ReadThreadingAssembler.java:114) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.LocalAssemblyEngine.runLocalAssembly(LocalAssemblyEngine.java:164) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.assembleReads(HaplotypeCaller.java:1022) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:882) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:218) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:708) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:704) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:273) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78) at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:314) 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)