It seems that the Orthofinder tool only accepts multiple FASTA files as input. These cannot be in a collection either, although the tool accepts data collections. The problem is that this makes it difficult to establish an automated workflow if no collection is accepted. At least when a FASTA collection is selected, the tool always aborts (Fatal error: Exit code 1).
If I manually extract the FASTA files from the collection and use them as input, it works. Wouldn’t it be good if the tool worked with a collection? Or am I making a mistake somewhere?
I have an older test history here with both an individual file run and a list collection run. I ran that with the collection identifiers that included a “.faa” at the end and one with that stripped off.
All three runs seem identical to me. Do you want to review to see if you notice anything else? You can share back a history too if you want to dig into this deeper together.
thank you very much for the quick and great help! It actually helped to solve the problem a bit It seems that the tool is working as it should and indeed it accepts collections, lists and single FASTA files. But for some reason I (but only sometimes) get an error when I provide it a collection/list. Here is my example: https://usegalaxy.eu/u/wennmannj/h/ortholog-detection-baculovirus-99-1
It seems that the tool is working as it should and indeed it accepts collections, lists and single FASTA files. But for some reason I (but only sometimes) get an error when I provide it a collection/list. Here is my example: