Attention:
The frontline support team will be unavailable to answer questions on April 15th and 17th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!

Code exception of HaplotypeCaller in gVCF mode

I am working on pig WGS data. When I generated gVCF from bam files, I encountered errors for some of the bam files. This command worked well for most of my bam files.

${JAVA} ${GATK}/GenomeAnalysisTK.jar -T HaplotypeCaller -R ${REF} \
-I ${INPUT}/${Sample}_mkdup_realn_recal.bam -nct $nprocs \
--emitRefConfidence GVCF --variant_index_type LINEAR \
--variant_index_parameter 128000 \
--dbsnp ${KNOWN}/susScr3_dbSNP138_NCBI.vcf \
-o ${VCF_dir}/${Sample}.g.vcf

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

java.util.ConcurrentModificationException
at java.util.LinkedHashMap$LinkedHashIterator.nextNode(LinkedHashMap.java:711)
at java.util.LinkedHashMap$LinkedEntryIterator.next(LinkedHashMap.java:744)
at java.util.LinkedHashMap$LinkedEntryIterator.next(LinkedHashMap.java:742)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.addMiscellaneousAllele(HaplotypeCallerGenotypingEngine.java:292)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assignGenotypeLikelihoods(HaplotypeCallerGenotypingEngine.java:262)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:941)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:218)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java: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$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

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

Answers

Sign In or Register to comment.