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Old 02-18-2016, 07:52 PM   #53
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Also, note this line:

Started 1 mapping thread.
This means it is running using only 1 thread. Depending on your input size, it could take a while! If that's intentional, then it's fine. But BBMap is fully multithreaded so normally I request all available slots on a node when scheduling, and tell BBMap to use all of them with the flag "threads=16" (for example). It will normally autodetect the number of available processors and use all of them, but on SGE/UGE (which I think you are using), if the NSLOTS environment variable is set, it will cap the max threads at that value (so for example on a 16-core machine, if you request 1 slot, such that "echo $NSLOTS" returns 1, then unless you manually specify the number of threads it will only use 1, to ensure fairness).

I recommend you ssh into the node it's running on and run "top -c", then look for a java process and ensure it is using CPU resources (should be at 100%). You can also examine the output file; it should gradually be growing.

Last edited by Brian Bushnell; 02-18-2016 at 07:55 PM.
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