[Biopython] Problems with Phylo/PAML/codeml.py in newer BioPython version

[Jeremy Chase]

Hi everyone,

I recently began transitioning my analyses from a big computing cluster
that currently has an older version of BioPython (1.59) to a local box that
I've installed the newest version of BioPython on (1.66). Unfortunately,
I'm now having some problems using codeml via Bio. I'm not sure if this is
due to differences between the two versions or simply a problem with how I
have things configured, and I was hoping someone might have an idea about
how to go about figuring that out. Incidentally, the version of python is
also different (2.7.3 on the cluster, 2.7.6 on the new system.) Here is the
error message when I get when I call cml.run() via the same script that
works fine on the other cluster:
Traceback (most recent call last):
  File "codemlscript.py", line 117, in <module>
    results = cml.run()
  File "/usr/local/lib/python2.7/dist-packages/Bio/Phylo/PAML/codeml.py",
line 186, in run
    Paml.run(self, ctl_file, verbose, command)
  File "/usr/local/lib/python2.7/dist-packages/Bio/Phylo/PAML/_paml.py",
line 145, in run
    stdout=subprocess.PIPE)
  File "/usr/lib/python2.7/subprocess.py", line 522, in call
    return Popen(*popenargs, **kwargs).wait()
  File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
    errread, errwrite)
  File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

Thanks very much for taking the time to read.

Cheers!
Jeremy
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