Help for installation of Secretomep

Question

[jessy.tricard]

Hello everybody,

I installed secretome, but i don't run. I haven't any problem when I run the files tests of secretomep but I have an error when I run on my files : "is missing features (psort_vect) ". I don't understand, can you help me !

Thank you for your help !

Answer 1

[Ira]

I recently ran into this issue myself. From what I can tell the cause of the problem is that multiple instances of psort cannot run at the same time. I found that I could fix the problem by changing the secretomep script to set MAXCPU to 1. This works but is very slow. You can achieve some degree of speedup if you allow multiple CPUs but restrict to just one psort process at a time. In my secretomep script I added the following modification. Look for the section of the script that looks like this;

while ( `ls -1 proc |& wc -l` > $allow_par )
     sleep 2
  end

And replace with this

while ( `ls -1 proc |& wc -l` > $allow_par )
     sleep 0.5
  end

while ( `ls -1 proc |& grep 'psort' |& wc -l` > 0)
    sleep 0.5
end