[solved] BioPython: CodeML FileNotFoundError: [WinError 2]

Question

[atapee]

I have been trying to run a basic codeML wraper, that I got from the Biopython cookbook, but it doesn't seem to be working. I have been getting the error FileNotFoundError: [WinError 2].

This is what the piece of code looks like:

def codeML(outfile):
    cml = codeml.Codeml()
    cml.alignment = "C:\\Users\\User\\Documents\\project\\codonal.fasta"
    cml.tree = "C:\\Users\\User\\Documents\\project\\newtree.nwk"
    cml.out_file = outfile
    cml.working_dir = "C:\\Users\\User\\Documents\\project"
    cml.set_options(seqtype=1,
            verbose=0,
            noisy=0,
            RateAncestor=0,
            model=0,
            NSsites=[0, 1, 2],
            CodonFreq=2,
            cleandata=1,
            fix_alpha=1,
            kappa=4.54006)
    results = cml.run()
    ns_sites = results.get("NSsites")
    m0 = ns_sites.get(0)
    m0_params = m0.get("parameters")
    print(m0_params.get("omega"))

And this is what the error looks like:

Traceback (most recent call last):
  File "C:\Python34\elgrando.py", line 155, in <module>
    codeML("rezultati.out")
  File "C:\Python34\elgrando.py", line 143, in codeML
    results = cml.run()
  File "C:\Python34\lib\site-packages\Bio\Phylo\PAML\codeml.py", line 186, in run
    Paml.run(self, ctl_file, verbose, command)
  File "C:\Python34\lib\site-packages\Bio\Phylo\PAML\_paml.py", line 143, in run
    stdout=subprocess.PIPE)
  File "C:\Python34\lib\subprocess.py", line 537, in call
    with Popen(*popenargs, **kwargs) as p:
  File "C:\Python34\lib\subprocess.py", line 858, in __init__
    restore_signals, start_new_session)
  File "C:\Python34\lib\subprocess.py", line 1111, in _execute_child
    startupinfo)
FileNotFoundError: [WinError 2]

Python usually gives this error when there is a problem with pathing, but I have checked it twice now and it works if I independently run CodeML. Could it be that python doesn't recognise Paml on my computer or it doesn't have access to it?

[GouthamAtla]

May be its not in the path i.e not added to Environmental variables?

[Ram]

Can you check the input files and ensure they have no access/security problems? Files downloaded from the internet may need to be "unblocked".

[atapee]

It could be the Environmental variables, but it would be strange since other biopython tools work.

I have been using these files with other Biopython tools, they are probably not the cause of the problem.

I have been able to reduce the errors to only one:

File "C:/Python34/standalone.py", line 2, in codeML
    cml = codeml.Codeml()
NameError: name 'codeml' is not defined

Still don't know what the problem is.

[Ram]

What does your import statement for codeML look like?

[atapee]

from Bio.Phylo.PAML import codeml

Well all the old errors are back, it had a random flash previously

[Ram]

Try reinstalling the CodeML package.

[Ram]

Hello atapee!

It appears that your post has been cross-posted to another site: http://stackoverflow.com/questions/28480506/python-biopythoncodeml-filenotfounderror-winerror-2

This is typically not recommended as it runs the risk of annoying people in both communities.

[atapee]

It has been deleted...

Answer 1

[atapee]

I think I have found the problem...

This is the control file that CodeML produces:

seqfile = kodonskaporavnava.fasta
outfile = results.out
treefile = novodrevo1.nwk
kappa = 4.54006
cleandata = 1
RateAncestor = 0
seqtype = 1
model = 0
noisy = 0
verbose = 0
fix_alpha = 1
NSsites = 0 1 2
CodonFreq = 2

There are not paths, only file names. If I look up the same file when produced by stand-alone CodeML it has full paths. CodeML apparently works, but it does not recognise the file paths... I have no idea why, because if I copy/paste them to a different biopython module, they work as intended.

*Sorry for the different file names, they are just in a different language.

[idowuolawoye]

Were you able to sort this out after finding out the issue? I have similar issue with the control file producing just the file names without adding the paths.