Hi @alfrhul
It sounds like you have done good troubleshooting. Reference for others about those checks: https://galaxyproject.org/support/
- Preparing and using a Custom Reference Genome or Build
- Mismatched Chromosome identifiers (and how to avoid them)
- Extended Help for Differential Expression Analysis Tools
The problem could be with the genome formatting issue still present, or the tool itself be running out of resources. RNA Star is a memory-intensive tool. I’m guessing the second but we can confirm. Format or content issues are the usual cause for tools ending with a server-side/resource type of error.
There was another reported problem with this tool at UseGalaxy.org around the same time frame that you wrote in. Their problem was the job not running at all. RNAStar not running
Meanwhile, for your case, perhaps start up a HISAT2 job using that same custom reference genome and annotation. Most mappers will not fail due to fasta format/content issues (when used alone) but incorporating reference annotation can reveal problems.
Run that job from the same history that the RNA Star failure is in, and please send in a bug report from one of the red error datasets. Please place a link to this Galaxy Help topic in the bug comments so we can link the two.
We are doing some checks administratively and will review bug reports around this tool. Feedback soon.