HISAT2 Tool Failing: Guidance for known issue at UseGalaxy.org Feb 9 2026. README

Welcome @axao

Thank you for reporting the error! Hopefully we can help!

Issue

This error with HISAT2 will present for some jobs and not others, and only at UseGalaxy.org.

We are working to correct the jetstream2 cluster configuration server side issue. The job container is incorrect. HISAT2 and Mutect2 are both impacted.

What to do

Reruns are working for me know, but the issue is not confirmed to be corrected yet.

You can also try a rerun if you would like, then let us know the status back here.

Remember: if your original job was part of a collection, or if it was executed with a workflow, there are additional toggles on the rerun tool form to replace results or to continue with the workflow, or both!

We’ll post more feedback here once fully confirmed to be resolved! :slight_smile: