how to specify number of threads parameter in GATK Haplotpyecaller command line ??

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Nikhil Gunala

• August 01, 2023 09:39
• Edited

REQUIRED for all errors and issues:
a) GATK version used: gatk4-4.4.0
b) Exact command used: gatk  HaplotypeCaller -I PLLD15-09214movieccssortedrg1.bam -R Gmax_508_v4.0.fa -ERC GVCF -nt 8 -O  PLLD1509214.g.vcf
c) Entire program log: A USER ERROR has occurred: '-nt' is not a valid command
Error : A USER ERROR has occurred: '-nt' is not a valid command

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  Gökalp Çelik

  • August 01, 2023 17:08

  Hi Nikhil Gunala

  GATK 4 release does not handle threading as GATK3 releases so -nct or -nt switches are no longer applicable to HaplotypeCaller and bunch of other tools that supported them before. 

  Our suggestion would be to scatter your genome to multiple intervals and running them in parallel in a scatter-gather way. 

  Of course if you still wish to use the threading and older GATK3 you may get them from the archive 

  https://console.cloud.google.com/storage/browser/gatk-software/package-archive/gatk;tab=objects?pli=1&prefix=&forceOnObjectsSortingFiltering=false 

  Keep in mind that these are very old releases and no longer supported. 

   

  Regards. 

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  Nikhil Gunala

  • August 02, 2023 05:09

  Hi Gökalp Çelik,

  Thank you very much for the information.

   

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  Geert Vandeweyer

  • December 05, 2023 07:05

  Hi Nikhil, 
  
  we've been using these settings to control threading in GATK 4+ (to some extend) : 
  - Haplotypecaller takes the option :  --native-pair-hmm-threads 4
  - CNNScoreVariants : through an env variable: export OMP_NUM_THREADS=16

   

   

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