Question and suggestion re -nct & -num_threads options


I'm trying to implement a workflow with GATK for the first time and I'm getting caught out by the -nct/-num_threads options not being compatible with all walkers, erroring and then killing the process.

Can I suggest that if the flags are not implemented/supported by a walker that the option is ignored. The docs don't clarify which walkers work and which don't so I need to test each one. It would be much easier if simply a warning message were given.

Also, I don't fully understand the difference between -nct/-num_threads. Can someone explain it, please?

Best Answer


  • drchriscoledrchriscole Posts: 16Member

    Thanks for the reply.

    It's a shame the -nct option can't be ignored if not (yet) implemented.

    Thanks for the clarification and I'll look forward to the new documentation.

  • nihilnihil Posts: 1Member


    I'm also very interested in that documentation. Any news about that?

    Best regards

  • frankfengfrankfeng Posts: 22Member

    Me too. Looking forward to that documentation. Thanks GATK team!

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 9,956Administrator, Dev admin

    Yes we've documented this since then, here and here.

    Geraldine Van der Auwera, PhD

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