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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


  • 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 Member


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

    Best regards

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

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

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

  • mbelmadanimbelmadani VancouverMember

    @Geraldine_VdAuwera said:
    Yes we've documented this since then, here and here.

    If I look at the parallelization table (Applicability of parallelism to the major GATK tools), I see that BaseRecalibrator only supports NCT, but if I run $GATK -T BaseRecalibrator --help

    ... The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50 ...
    -nt,--num_threads <num_threads> Number of data threads to to this analysis
    -nct,--num_cpu_threads_per_data_thread <num_cpu_threads_per_data_thread> Number of CPU threads to per data thread

    Both -nt and -nct appear in the help menu. Is it safe to use both -nt and -nct, or is it not recommended to use options that aren't described on the GATK online documentation (e.g. Like the HaplotypeCaller, where -nct appears in the help menu but is not recommended/stable)? Speaking of HaplotypeCaller, the -nt argument also shows up in the --help menu. Do these just appear somewhat automatically regardless if they're supported or not, or are options displayed in the --help menu supported?

    Thank you

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @mbelmadani Unfortunately because of how the engine arguments are wired up, these both appear for all tools, but they don't actually work with all tools. The individual Tool Docs specify what can be used or not.

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