David Emms

Hi Olivia Could you paste the full log from the start of the run please, it may contain a clue as to what caused the problem. All the best David

Hi @biology-han I've deleted your message as it is not relevant to this issue. If you have an issue could you please post it as a new issue and provide...

Hi I think this might be because OrthoFinder needed an update to work with python 3.11. It was reported here and has now been resolved: https://github.com/davidemms/OrthoFinder/issues/782 Is that the same...

Hi Liam The latest release has an option `--fewer-open-files` that should resolve this: https://github.com/davidemms/OrthoFinder/releases/tag/2.5.5 Best wishes David

(The option will become default in the 3.0 release)

Hi Unfortunately I don't know what this about, OrthoFinder doesn't use Open MPI or CUDA, I think this is probably from something else. Best wishes David

Hi I'd like to dig into this a bit more, do you have the full output produced by orthofinder? Or if not, do you know at what stage of the...

Hi @LucieGL Care should be taken with creating phylogenies from orthogroups with more than one gene per species since not all genes will be orthologs. There will not only be...

I've got a script for extracting just sets of orthologs, I'll try and upload it this week.

Hi Eric Thanks for letting me know. No, that wasn't intended, I'll make sure it's included in all future releases. Best wishes David