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.
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).
I assume 28gb is enough ram? I actually have a fast disk storage as well so I guess it doesn't matter. Thank you.
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.
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.
I've never had a problem running with more than 4 threads. You can definitely use 12.
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