jobscript is setting the memory per core at --mem-per-cpu 5000
This is ridiculously high for bwa, which should not be using much more than 5-9GB or ram for the run. It is also preventing bwa from getting on anything but the top end boxes which is slowing things down
ryanrichholt
commented
6 years ago
jobscript is setting the memory per core at --mem-per-cpu 5000
This is ridiculously high for bwa, which should not be using much more than 5-9GB or ram for the run. It is also preventing bwa from getting on anything but the top end boxes which is slowing things down
I would set it to 2000 or 3000 at the most