Issue with running Codeml using Biopython

Question

[laurenmee17]

Hi there

This is my first post so please be kind if my terminology is incorrect!

I've been trying to run a python script that uses the BioPython module Phylo.Paml to try and automate codeml on a number of alignments.

Here is my script (in progress)

    #!usr/bin/python

import sys
from Bio.Phylo.PAML import codeml

#USAGE python Practice.py aln tree ctrl output

print(sys.argv[1])
cml = codeml.Codeml(alignment = sys.argv[1], 
        tree = sys.argv[2],
        out_file = sys.argv[4],
        working_dir = ".")

cml.run()
ctl_file = sys.argv[3]
verbose = TRUE

Wrote as per direction from the BioPython.Phylo.PAML page (https://biopython.org/wiki/PAML)

This code works when I use it singly but not as I want it to. The console freezes as if the script is running indefinitely and does not stop until I cancel it. When I do I get this error message

Traceback (most recent call last):
  File "Practice2.py", line 14, in <module>
    cml.run()
  File "/home/mee/miniconda3/lib/python3.6/site-packages/Bio/Phylo/PAML/codeml.py", line 182, in run
    Paml.run(self, ctl_file, verbose, command)
  File "/home/mee/miniconda3/lib/python3.6/site-packages/Bio/Phylo/PAML/_paml.py", line 121, in run
    result_code = subprocess.call([command, ctl_file], stdout=dn, stderr=dn)
  File "/home/mee/miniconda3/lib/python3.6/subprocess.py", line 269, in call
    return p.wait(timeout=timeout)
  File "/home/mee/miniconda3/lib/python3.6/subprocess.py", line 1457, in wait
    (pid, sts) = self._try_wait(0)
  File "/home/mee/miniconda3/lib/python3.6/subprocess.py", line 1404, in _try_wait
    (pid, sts) = os.waitpid(self.pid, wait_flags)
KeyboardInterrupt

But when I check my working directory all the output files of the run are waiting there. Similarly, if I cancel the command quickly enough and initiate codeml I am taken to a working screen where codeml is actively running through the files I have input into the script.

Help!

[Joe]

Could you explain a little more what you mean by,

This code works when I use it singly but not as I want it to.

I don't thing your verbose = TRUE line is doing anything FYI. You should be running it as cml.run(verbose=True). Could you do that and post what output you get in that case?