Error : While Running Muscle In Windows

Question

[Edison]

Hi,

I am getting error while running muscle in windows.

c:\Program Files \ muscle>muscle3.8.31_i86win32.exe  -in seqs.fa -out seqs.afa
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.
seqs 2 seqs, max length 71, avg  length 71
00:00:00      3 MB(0%)  Iter   1  100.00%  K-mer dist pass 1
00:00:00      3 MB(0%)  Iter   1  100.00%  K-mer dist pass 2
00:00:00      4 MB(0%)  Iter   1  100.00%  Align node
00:00:00      4 MB(0%)  Iter   1  100.00%  Root alignment
*** ERROR ***  Cannot open 'seqs.afa' errno=13

Please help me to solve this error.

Answer 1

[Jan Kosinski]

Running this way muscle would try to save seqs.afa to c:\Program Files \ muscle> folder. On Windows, if you run muscle not as administrator, you may have not permission of writing to c:\Program Files \ muscle>, hence the error.

You can try copying the seqs.fa to Desktop. Then navigate to Desktop in command prompt and execute muscle this way:

c:\Users\you\Desktop> c:\Program Files \ muscle\muscle3.8.31_i86win32.exe -in seqs.fa -out seqs.afa

Note the full path to muscle. If it works you can modify PATH environmental variable (check google how to do it for your windows version) so you could write just muscle\muscle3.8.31_i86win32.exe in the command prompt.

[Edison]

Thank you very much for your answer.