What's the maximum number of threads that bwa mem can handle?

Question

[anp375]

I remember reading that if we go beyond 4, something gets messed up - either the alignment, or an error is thrown. I can't find this info however. I want to use -t 12.

[GenoMax]

Unless you have a fast disk storage system I/O may become a limiting factor (assuming you have ample RAM available to allocate to 12 threads).

[anp375]

I assume 28gb is enough ram? I actually have a fast disk storage as well so I guess it doesn't matter. Thank you.

[GenoMax]

You will find out as you start running. If some of the threads remain in (non-R state in "top -H") then that would be a clue.

[harold.smith.tarheel]

RAM may become limiting, depending upon the sequence composition of your reads and the reference genome. My recollection is that the reference is loaded only once (~4 GB) but the alignment data load scales with the number of threads (~2-3 GB per thread). Heng may provide a more accurate response if you post to the BWA mailing list.

Answer 1

[DG]

I've never had a problem running with more than 4 threads. You can definitely use 12.