Code exception at Haplotypecalle step.

Here is my command I actually used.

java -jar -Xmx39g $gatk -T HaplotypeCaller -l INFO -R $reference -I $sample.bam --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 --dbsnp $dbsnp -o $sample.raw.snps.indels.g.vcf -S LENIENT > $sampleName""$processDay""HaplotypeCaller.log 2>&1 &&

I'm trying to use Haplotypecaller on some whole genome projects. There is no any error from mapping to BQSR. However, such error message happened ramdomly in term of the location of genome and subjects. Some subjects can be finished without any error by the same script. Could anyone give some idea about what was happened ?

ERROR ------------------------------------------------------------------------------------------

ERROR stack trace

java.util.ConcurrentModificationException at java.util.LinkedHashMap$LinkedHashIterator.nextEntry(Unknown Source) at java.util.LinkedHashMap$EntryIterator.next(Unknown Source) at java.util.LinkedHashMap$EntryIterator.next(Unknown Source) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.addMiscellaneousAllele(HaplotypeCa at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assignGenotypeLikelihoods(Haplotyp at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:941) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:218) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471) at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source) at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source)

ERROR ------------------------------------------------------------------------------------------

ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee):

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 ------------------------------------------------------------------------------------------