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HaplotypeCaller crash with multithreading + SSE

johnwallace123johnwallace123 ✭✭Member ✭✭

I recently ran the HaplotypeCaller using both the new --pairHMM options and -nct 2, and I encountered a crash in the program (8 of 96 runs crashed). I have rerun the analysis without the "-nct 2" option, and it appears to work as expected, so I'm not in a hurry. I am currently using GATK 3.1-1; below is the specific command I used as well as the stack trace that resulted.

Command:
GenomeAnalysisTK -T HaplotypeCaller -R human_g1k_v37_decoy.fasta -I [email protected] --dbsnp dbsnp_137.b37.vcf.gz -L targets.GRCh37.bed -A QualByDepth -stand_emit_conf 10 -mbq 20 --downsample_to_coverage 300 -A HaplotypeScore -A MappingQualityRankSumTest -A ReadPosRankSumTest -A FisherStrand -A GCContent -A AlleleBalanceBySample -A AlleleBalance -o HG00593.vcf.gz -sample_rename_mapping_file rename_file -nct 2 -ERC GVCF -pairHMM VECTOR_LOGLESS_CACHING -variant_index_type LINEAR -variant_index_parameter 128000

Stack trace:

ERROR stack trace

java.util.ConcurrentModificationException
at java.util.LinkedHashMap$LinkedHashIterator.nextEntry(LinkedHashMap.java:394)
at java.util.LinkedHashMap$EntryIterator.next(LinkedHashMap.java:413)
at java.util.LinkedHashMap$EntryIterator.next(LinkedHashMap.java:412)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.addMiscellaneousAllele(GenotypingEngine.java:257)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.assignGenotypeLikelihoods(GenotypingEngine.java:227)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:880)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:141)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$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:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:722)

If you require anything else from me, please let me know.

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