[Possible Bug] The `-og` option doesn't stop after inferring orthogroups

[StefanFlaumberg]

Dear OrthoFinder team,

The manual states that using the -og option makes the program stop after inferring orthogroups, however, the observed behaviour is stopping only after having written sequence files for the inferred orthogroups (in the Orthogroup_Sequences folder). It also creates a folder with single-copy orthologue sequences (Single_Copy_Orthologue_Sequences) and an empty folder Orthologues. Thus, invoking the -og option is almost identical to using the -os option, the latter is different only in writing the same sequence files also in the WorkingDirectory folder.

Bug or not, writing the orthogroup sequence files may be redundant for some analyses (e.g. gene family presence/absence analysis), so it would be practical to have an option not to write these files. It may also be useful to have an option to clear up the WorkingDirectory folder after completing a run.

Thank you!

Best regards, Stefan

[davidemms]

Hi Stefan

Thanks for pointing reporting this, we will look into it.

All the best David