I am running dmpfold, "seq2maps.sh" and from a few days the program is at the "PSICOV" stage:

psicov -z 15 -o -d 0.03 tail-fiber-sequence.aln

"ps aux" gives me this:

daniel     26693  490  2.5 2546588 2514320 ?     Rl   سبت20 25116:58 psicov -z 15 -o -d 0.03 tail-fiber-sequence.aln

Any idea on what could be the matter? Yes, I am runinng "rosetta" too on my 32 CPUs, so all my CPUs are covered to max 100%; howver, RAM is 93Gb and only 32 GB has been used. Thanks


1 Answer 1


In summary just be patient. psicov doesn't parrallelise so a tenfold increase in CPU will not hurry it along.

Also psicov is not RAM intensive given the machine you are describing, so you haven't hit a RAM bottleneck.

I don't know the ps output format you are using I'm use to seeing %CPU and %MEM from ps -aux on Susie and OSX. You should also try,

top -c -u username

or for OSX top -u

You should see the psicov happily chuntering away consuming ~100% of a single process. There is a UNIX/Linux guru specialist on BioSE who could almost certainly provide better diagnostics.


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