I started a panaroo job with 3 .gff genome annotation files. Unfortunately, it kept aborting with the following error messages all related to “file not found” issues.
Does anyone know what I can do to fix this?
Thank you!
Hi @vera.thiel ,
your input datasets need to have their names ending in .gff (very unusual for a Galaxy tool, I know).
This topic: Panaroo & PanTA: sample recognition troubleshooting has more details including an example of how to change the names.
Sorry for the inconvenience,
Wolfgang
Dear Wolfgang,
thank you for your reply and help. Although the files were all .gff this seems to be the solution. I changed the name of the collection to end on .gff too and was able to start the job without the previously observed error message.
Thank you! 
Yes, this particular tool is a bit special. The “names” or element identifiers for files usually doesn’t matter, only the datatype! But this one couldn’t be made to work that way .. yet!
Glad you have this working now and thanks for letting us know! 