error mcl -9 no such file "clusters_OrthoFinder_I1.5.txt"

[cpouchon]

Hi,

I got this error when running orthofinder:

ERROR: external program called by OrthoFinder returned an error code: -9
Command: mcl /home/users/p/pouchon/OrthoFinder/Results_Nov12/WorkingDirectory/OrthoFinder_graph.txt -I 1.5 -o /home/users/p/pouchon/OrthoFinder/Results_Nov12/WorkingDirectory/clusters_OrthoFinder_I1.5.txt -te 2 -V all
stdout
------
b''
stderr
------
b''
2024-11-14 09:47:40 : Ran MCL
[Errno 2] No such file or directory: '/home/users/p/pouchon/OrthoFinder/Results_Nov12/WorkingDirectory/clusters_OrthoFinder_I1.5.txt'

I have tried to rerun the program, but I have the same issue.

Do you have any idea on that? Looking forward for your reply

Cheers

Charles

[lauriebelch]

Hi Charles,

Can I ask for the full orthofinder command that you used? and which version of orthofinder

[cpouchon]

Hi Laurie, of course. I installed via conda:

orthofinder 2.5.5

This is the command used:

TRANSDECODER_PATH=/home/users/p/pouchon/transdecoder/
ORTHOFINDER=~/miniforge3/bin/orthofinder

${ORTHOFINDER} -f ${TRANSDECODER_PATH}/transdecoder/

[lauriebelch]

Could there be a pathing error? I don't see /transdecoder in the path that MCL is looking in.

Would you be able to try the example data

[cpouchon]

I have not write all the path in the error message here for the example. The path to the data is correct. I can read the OrthoFinder_graph.txt file, but I think that the mcl command was not executed as I have no outputs

[cpouchon]

Hi Laurie, I have try to run manually MCL and it was a memory issue.