HaplotypeCaller : stack trace java.lang.ArrayIndexOutOfBoundsException: 97

Hi,

I've run HaplotyceCaller and after a while it errors out. I have checked the bam file with ValidateSamFile and no errors were found. I haven't been able to figure out the issue so I hope you can give me a hint

Thanks!

time java -Xmx4g -jar /home/joydeep/bin/gatk-2.5-2/GenomeAnalysisTK.jar -T HaplotypeCaller -R ucsc.hg19.fasta --dbsnp dbsnp_137.hg19.vcf -I JN001.bam -o JN001.raw.vcf -A AlleleBalance -A ReadPosRankSumTest -A QualByDepth -A HomopolymerRun -A FisherStrand --max_alternate_alleles 1 -l INFO

and got:

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.ArrayIndexOutOfBoundsException: 97
at org.broadinstitute.sting.utils.fragments.FragmentUtils.mergeOverlappingPairedFragments(FragmentUtils.java:256)
at org.broadinstitute.sting.utils.fragments.FragmentUtils.mergeOverlappingPairedFragments(FragmentUtils.java:200)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.finalizeActiveRegion(HaplotypeCaller.java:814)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.assembleReads(HaplotypeCaller.java:636)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:564)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:135)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegion(TraverseActiveRegions.java:564)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegions(TraverseActiveRegions.java:521)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:251)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:70)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:100)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:286)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.5-2-gf57256b):
ERROR
ERROR Please check the documentation guide to see if this is a known problem
ERROR If not, please post the error, with stack trace, to the GATK forum
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: 97
ERROR ------------------------------------------------------------------------------------------

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