A program "PSICOV" "stopped" from a few days on Ubuntu 18.04? 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
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.