Muscle - errno 2 - can't open the file

Question

[icebreaked]

Hello guys,

I would like to use the software 'MUSCLE'. I run this software via a perl script. This software returns the following error:

 MUSCLE v3.8.31 by Robert C. Edgar
http://www.drive5.com/muscle
This software is donated to the public domain.
Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.


*** ERROR ***  Cannot open '../seq.faa' errno=2

I don't understand what this error means ('errno = 2'). I searched it but I didn't find anything. Do you have any idea what does this error mean ?

Thank you in advance for your answers :)

Best regards

[Michael]

Please be more specific:

• what is the actual command line used?
• what is in that perl script?

Without this information, we will be unable to help you further.

[Joe]

Double check that your file also has some sequence in it and hasn't been overwritten/made blank some how. Also double check it's formatting?

[h.mon]

Can you run Muscle with ../seq.faa on the command line? If not, probably your file is the culprit - corrupted or badly formated.

[WouterDeCoster]

Does the file ../seq.faa exist? Is the path correct? Can you try with the absolute path?

[icebreaked]

Thanks for your answer, WouterDeCoster. I tried the absolute path but I have the same error. I'm sure that the file exists but I don't have any idea why it's not working.

[WouterDeCoster]

Do you have permission to read and or write to the file?

Could you try:

import os
os.path.isfile("/path/to/seq.faa")

[Michael]

Op is using a Perl script...

[WouterDeCoster]

Right, naive expectation.