Hi I am trying to run haplotypecaller to generate the gVCF file for one sample and it always fail if i use threading. Here is the command i am using I am using GATK 3.1-1 for reference and it runs fine no threads.
-T HaplotypeCaller -R /data2/bsi/reference/sequence/human/ncbi/hg19/allchr.fa --emitRefConfidence GVCF -variant_index_type LINEAR -variant_in dex_parameter 128000 -nct 12 -I .bam -o .threads.gVCF
ERROR :
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
java.util.ConcurrentModificationException at java.util.LinkedHashMap$LinkedHashIterator.nextEntry(LinkedHashMap.java:390) at java.util.LinkedHashMap$EntryIterator.next(LinkedHashMap.java:409) at java.util.LinkedHashMap$EntryIterator.next(LinkedHashMap.java:408) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.addMiscellaneousAllele(GenotypingEngine.java:257) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.assignGenotypeLikelihoods(GenotypingEngine.java:220) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:880) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:141) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:708) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:704) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) at java.lang.Thread.run(Thread.java:722)
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.1-1-g07a4bf8):
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: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------
Could you let me know if there is bug in threading or i am doing something wrong in GATK invocation.
Thanks Saurabh