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Muscle - errno 2 - can't open the file

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

muscle perl
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updated by Michael Dondrup Michael Dondrup • written by icebreaked • icebreaked

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

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written by WouterDeCoster WouterDeCoster

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.

• 0 views • link
written by icebreaked • icebreaked

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

Could you try:

import os
os.path.isfile("/path/to/seq.faa")
• 0 views • link
written by WouterDeCoster WouterDeCoster

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.

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written by Michael Dondrup Michael Dondrup

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?

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written by Joe Joe

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

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written by h.mon h.mon

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