GATK 3.0 HaplotypeCaller RUNTIME ERROR
Posted in Ask the GATK team | Last updated on 2014-03-19 15:37:30

Comments (11)


I am running Haplotypecaller for ~600 bams to perform gVCF call on a cluster (SGE qsub system). Each node has 32 cores, 256 GB RAM. I am running 8 tasks pernode, so each task has 4 cores and 32GB memories.

It's been running ~30 hours now (a single BAM needs ~5 hours), out of the ~500 finished tasks there are 24 quit with error showing below. I am not sure if it is an error caused by my command or something else. Can someone give any suggestions?

The command:

java -Xmx32G GATK3.0 \ -T HaplotypeCaller \ -ERC gVCF -L EZ_Exome_v2.bed \ -variant_index_type LINEAR \ -variant_index_parameter 128000 \ -R ucsc.hg19.fasta \ -nct 4 \ --dbsnp dbsnp_138.hg19.vcf \ -I 1.recalibrated.bam \ -o 1.recalibrated.vcf

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

java.util.ConcurrentModificationException at java.util.LinkedHashMap$LinkedHashIterator.nextEntry( at java.util.LinkedHashMap$ at java.util.LinkedHashMap$ at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.addMiscellaneousAllele( at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.assignGenotypeLikelihoods( at at at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply( at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply( at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$ at java.util.concurrent.Executors$ at java.util.concurrent.FutureTask$Sync.innerRun( at at java.util.concurrent.ThreadPoolExecutor.runWorker( at java.util.concurrent.ThreadPoolExecutor$ at

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.0-0-g6bad1c6):
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
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

thanks a lot!

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