prody
Direct coupling analysis error
I'm trying to run some multiple sequence alignment analyses with ProDy, but when I run the command "buildDirectInfoMatrix" I get an error that states "Python has stopped working. A problem caused the program to stop working correctly. Please close the program". Is this a problem on my end, or a problem with the command?
I'm running Python 3.5.6 on a Windows machine in a Jupyter notebook. I am able to successfully run other multiple sequence alignment analyses such as buildSCAMatrix. Below is an example of my input:
msa = parseMSA('cytc.fasta') msa_refine = refineMSA(msa, label=None, rowocc=None, seqid=None, colocc=1) direct_info =buildDirectInfoMatrix(msa_refine, seqid = 0.8, psuedo_weight= 0.5)
--> This produces the error, and then my kernel in my Jupyter notebook dies and has to be restarted.
In contrast, this command works the way I want it to: msa = parseMSA('cytc.fasta') msa_refine = refineMSA(msa, label=None, rowocc=None, seqid=None, colocc=1) SCA = buildSCAMatrix(msa_refine, turbo=True)
It may be that the process is too memory intensive and the Jupyter notebook can't handle it. Could you try using a terminal instead and see if that works?
I ran it in a terminal, but I get the same error. Do you know of any other ways to check if the error is caused by insufficient memory?
You could maybe try running top or htop in another terminal and see how much memory it uses.
Checking whether you ran out of memory isn't going to help you to not use too much memory. John (SHZ66) is going to look into the C/C++ code to fix it. He thinks he knows what the problem is and that it's related to using windows.