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davidemms / OrthoFinder

Phylogenetic orthology inference for comparative genomics
https://davidemms.github.io/
GNU General Public License v3.0
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Question_process_Orthofinder #911

Open cristoyerenahs opened 1 week ago

cristoyerenahs commented 1 week ago

Good Afternoon. Orthofinder team.

I have run the Orthofinder (./orthofinder -f mydata) process with 1000 proteomes of different bacteria species, After some days, I had some erros in order to generate the outputs files.

I want to attach the errors.

Could you help about the erros?

Thanks erros

Jonathan-Holmes-Bioinformatics commented 1 week ago

Hi cristoyerenahs,

OrthoFinder was built for handling eukaryotic genomes in smaller batches than you are working on (1000). It looks like the issue is due to the program opening to many files during its multiprocessing stage for writing the Orthogroup matrices.

I would recommend trying some of the solutions on this thread:

https://stackoverflow.com/questions/16526783/python-subprocess-too-many-open-files

Hope this helps.