Hi
I tried to call variant (HaplotypeCaller) after finishing Recalibrate(PrintReads) command.
below is my command
java -Xmx512m -Djava.io.tmpdir=./tmp/ -jar ../GenomeAnalysisTK.jar -T HaplotypeCaller -R ./chr22.fa -nct 7 -I ./SRR341919.subset.sort.dedup.addrg.realigned.recal.bam --genotyping_mode DISCOVERY -stand_emit_conf 10 -stand_call_conf 30 -o ./SRR341919.subset.vcf
but I am confused since i got the error message below.
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
java.lang.IndexOutOfBoundsException: Index: 25, Size: 8
at java.util.LinkedList.checkElementIndex(LinkedList.java:553)
at java.util.LinkedList.get(LinkedList.java:474)
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$ReadMapReduceJob.run(NanoScheduler.java:471)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:744)
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.2-0-g289df4b):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, 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: Index: 25, Size: 8
ERROR ------------------------------------------------------------------------------------------
I think it might be a problem with array indexing but i can't solve by myself.
And i also saw previous posts that these similar problems can be fixed by releasing new version but my version is the latest version!
I don't know why i was trapped in this problem. I also guess my bam files have some problems but when i tried to another call variants(UnifiedGenotype) , there are no error and i have a results with vcf files.
So.. i don't know
I need your help
Thank you.