I am trying to run HISAT2 for paired-end trimmed FASTQC datasets with the EBV reference genome, but all HISAT2 jobs fail immediately. The error message says, "/jetstream2/scratch/main/jobs/…/tool_script.sh: line 10: hisat2-build: not found, and Fatal error: Exit code 127.” I have tried using “Use genome from history” with the EBV FASTA, creating paired dataset collections, and both single- and paired-end options, but it still fails. It seems like the HISAT2 tool on the server may be missing or misconfigured. Does anyone know what I could do at this point?
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! 
Update! Reruns will work using a different version of HISAT2 (“older” by about a week).
Use for now: HISAT2 A fast and sensitive alignment program(Galaxy Version 2.2.1+galaxy1)
Avoid until this topic closes out: HISAT2 A fast and sensitive alignment program(Galaxy Version 2.2.2+galaxy0)
How to toggle into a different tool version
- Load up the tool form, or go into the workflow editor
- Use the Versions menu
- FAQ: Changing the tool version