David Emms

Hi DIAMOND is crashing when 'blasting' some of your input files against each other (orthofinder uses the input proteomes but just renames the sequences with short IDs of the form...

Hi Could it be that your input files are somewhere where OrthoFinder doesn't have read/write access? What happens if you put the input files in your home directory? Best wishes...

Hi Thanks for the report. I wonder if this is perhaps I python 3.8 related issue. Bioconda just upgraded to using python v 3.8 in the last week. Could you...

Hi aziele This currently isn't possible, if you were to resolve the problem of separate pairwise files then there are other scaling issues linked to computation requirements (RAM, runtime) that...

Hi Could you email me your Duplications.tsv file, or just the first and last 10 lines if the file is very large. You can use [email protected]. OrthoFinder is trying to...

Just to follow up on this, @matrs is correct about this for the "-M msa" option. If you don't use that option, then OrthoFinder uses the STAG algorithm for species...

Hi Marcus Are you able to share the full OrthoFinder output so I can see if there's any indication of the problem? Best wishes David

Hi I'd need the full logs in order to investigate this. It looks like the diamond (default) or blast search failed. This could be because there is a problem with...

Hi Rauf Thanks, and I appreciate the feedback. I think this is probably due to the tree inference and/or the MSA inference and therefore best resolved by providing a fixed...

Hi I think you might be running an old version and this issue has been fixed in the latest version (2.5.4). All the best David