single copy orthologues list incorrect?

[s-tran94]

Hello,

So I recently ran an OrthoFinder run with four different plant species using version 3.0.1b1 installed via Conda on my institution's cluster. However, when I go to look at the Orthogroups_SingleCopyOrthologues.txt ouput file, I am seeing some listed orthogroups that clearly have multiple genes from a single species. I have cross-checked this list with the full list of orthogroups in the N0.tsv output file, which is leading me to believe that the gneerated list of single copy orthologs might be incorrect.

Does anyone know if I am doing anything incorrectly? I am fairly new to using this program so any help is greatly appreciated!

Sorrel