I noticed an issue with Bowtie2 that’s new. I haven’t thoroughly checked it out, but it seems that mapping seems to work with a built in reference, but a custom reference that I’ve been using throws an error.
Hi @Jon_Colman
The error message points on issue with the fasta file:
Warning: Empty fasta file
Preview (eye icon) does not work on the file. Something is wrong. Ping @jennaj , I cannot see the fasta file. Is it a storage related issue?
Jon, can you upload the file again? If you have this file in Galaxy, in another history, check it with Preview. If you see the content, you probably can use it.
It is night time in the US. I hope the issue will be addressed in the morning.
Kind regards,
Igor
Ok, I see this now. I looked at several of my saved reference files that I keep in a separate folder, several but not all have the same issue.
Thanks Igor
Thanks for the ping @igor and @Jon_Colman we know about some problems over the weekend through today. See this topic for the details → Too many errors: UseGalaxy.org downtime Sept 29 2025 -- Update topic! - #2 by jennaj. I’ll be posting updates until fully resolved.