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GenotypeGVCFs multithread not working properly

Hi GATK team,
I ran the haplotypcaller on a single mapped bam file. Command:

java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I MyMappedSample.bam --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -o MyMappedSample.g.vcf -L hg38.exome.regions.bed

From this output, I am running the GenotypeGVCFs. Command:

java -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -R Homo_sapiens_assembly38.fasta --variant MyMappedSample.g.vcf -o MyMappedSample.geontyped.vcf -nt 32 -L hg38.exome.regions.bed

The issue that I am is that when running the GenotypeGVCFs, even though I have the "-nt" flag, it is not using multiple threads, and only running with a single thread. I am only running this on a single sample. I am using version 3.5 (we have not yet updated our system to a java 8). Is this an issue with version 3.5, and I should maybe try an earlier version?

Issue · Github
by Sheila

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  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    This is unlikely to be a GATK problem; it's more likely that your system does not support multithreading or does not have access to multiple cores. Multithreading does work automatically on all systems.

  • Thank you for your response. Our system does support multithreading. It seems that it is just this 1 module of GATK that doesn't work with the multithreading. Everything else that can use a multithread does work (including other non-GATK applications). Oddly, when I add the "-nt" flag it tells me that it will take ~5hrs to finish, but without this flag it will finish it ~5 min...Not sure what it going on here.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator


    Have a look at Geraldine's response in this thread from February 25th.


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