6 months ago by
This is the same issue here, correct? https://biostar.usegalaxy.org/p/25246/
I am assuming that other tools work and general configuration of your instance is intact. And that you contacted the tool authors to get help with original config problems.
Data not being found in the working directory - or that directory not being created for some reason (permissions?) - could be a factor. It may even be that some intermediate working file is empty or is referenced incorrectly with the tool wrapper. Or some server/cluster issue - I've seen tools error this way when the working area has run out of space. Check those first, then contact the tool authors to work through this error with you.
Thanks, Jen, Galaxy team