Question and suggestion re -nct & -num_threads options

drchriscole

Hi,

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? TIA

Geraldine_VdAuwera

Setting up the argument collector to ignore options is unsafe, we won't do that. But we are planning to add that information (which modes are supported) to the documentation.

We'll have a document explaining -nct vs -nt up very soon. In the meantime, what you need to know is that -nct is the number of CPU threads, ie threads that can be run by different cores if you have a multicore CPU, while -nt is the number of data threads, ie number of "clones" of the GATK that are run in parallel on your machine.

We'll also provide a table of recommendations for which modes to use and how to tweak performance for the major GATK walkers.

drchriscole

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.