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

**URL:** <https://help.galaxyproject.org/t/hisat2-tool-failing-guidance-for-known-issue-at-usegalaxy-org-feb-9-2026-readme/17436>\
**Category:** usegalaxy.org support\
**Tags:** server-open-issue, hisat2\
**Created:** [February 10, 2026, 6:30am UTC](https://help.galaxyproject.org/t/hisat2-tool-failing-guidance-for-known-issue-at-usegalaxy-org-feb-9-2026-readme/17436 "2026-02-10T06:30:56Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![axao](https://avatars.discourse-cdn.com/v4/letter/a/e19b73/32.png) [@axao](https://help.galaxyproject.org/u/axao)\
**Post date:** [February 10, 2026, 6:30am UTC](https://help.galaxyproject.org/t/hisat2-tool-failing-guidance-for-known-issue-at-usegalaxy-org-feb-9-2026-readme/17436/1 "2026-02-10T06:30:57Z")

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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?

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [February 10, 2026, 7:13pm UTC](https://help.galaxyproject.org/t/hisat2-tool-failing-guidance-for-known-issue-at-usegalaxy-org-feb-9-2026-readme/17436/2 "2026-02-10T19:13:22Z")

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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](http://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](https://galaxyproject.github.io/training-material/faqs/galaxy/datasets_icons.html) tool form to replace results or to continue with the workflow, or both!

- [Rerunning only failed jobs in a workflow: Replace and Resume functions - #2 by jennaj](https://help.galaxyproject.org/t/rerunning-only-failed-jobs-in-a-workflow-replace-and-resume-functions/16387/2)

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

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [February 10, 2026, 10:07pm UTC](https://help.galaxyproject.org/t/hisat2-tool-failing-guidance-for-known-issue-at-usegalaxy-org-feb-9-2026-readme/17436/3 "2026-02-10T22:07:08Z")

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**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

1. Load up the tool form, or go into the workflow editor
2. Use the **Versions** menu
3. [FAQ: Changing the tool version](https://galaxyproject.github.io/training-material/faqs/galaxy/tools_change_version.html)