[Biopython] Problems with Phylo/PAML/codeml.py in newer BioPython version
Brandon Invergo
b.invergo at gmail.com
Fri Mar 18 10:10:13 UTC 2016
Hi Jeremy,
On Thu, 2016-03-17 at 20:52 -0700, Jeremy Chase wrote:
> 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
It looks like codeml isn't in your PATH. Verify that you can run it
from the commandline. Alternatively, you can use the "command" option
to the "run" method to manually specify the location of the codmel
binary.
-brandon
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