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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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Conda environment diamond version is super old (0.9.10)? #927

Closed shjenkins94 closed 1 month ago

shjenkins94 commented 1 month ago

Tried installing Orthofinder from mamba today, and when I was trying to figure out why I kept getting core dump errors I noticed that it installed diamond 0.9.10.

Might be a python 3.11 issue?

davidemms commented 1 month ago

Hi

I had to restrict the diamond version somewhat - details below. For OrthoFinder 2.5.5 onwards the requirement is diamond <2.1|>=2.1.7: https://github.com/bioconda/bioconda-recipes/blob/ff67f895fce2af5c6e72bf176510b88224cc8234/recipes/orthofinder/meta.yaml So I think this means that you should be able to use a newer version of diamond too. What happens if you try conda install -c bioconda 'diamond>=2.1.7' in your environment?

Also, was this a fresh conda environment or an existing one? I wonder if it's installing an old version of diamond by default?

DIAMOND Version Issue: There was an issue with a number of diamond versions whereby it would fail with an error if the proteome didn't pass a check, which many common & reasonable proteomes failed. There was a then an option to turn this off - but this option itself caused an error if it was a version of diamond that didn't know about this option! To avoid this orthofinder avoids these versions.

All the best David

shjenkins94 commented 1 month ago

Huh, I tried mamba create -n orthofinder orthofinder today and the problem seems to be gone. Something might've been wrong with one of the other dependencies or something but it works now