# HISAT2 jobs remain gray / new for approximately 23 hours on usegalaxy.org

**URL:** <https://help.galaxyproject.org/t/hisat2-jobs-remain-gray-new-for-approximately-23-hours-on-usegalaxy-org/18516>\
**Category:** usegalaxy.org support\
**Tags:** queued-gray-datasets\
**Created:** [October 20, 2026, 2:11pm UTC](https://help.galaxyproject.org/t/hisat2-jobs-remain-gray-new-for-approximately-23-hours-on-usegalaxy-org/18516 "2026-10-20T14:11:17Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![linhhmo](https://avatars.discourse-cdn.com/v4/letter/l/a87d85/32.png) [@linhhmo](https://help.galaxyproject.org/u/linhhmo)\
**Post date:** [October 20, 2026, 2:11pm UTC](https://help.galaxyproject.org/t/hisat2-jobs-remain-gray-new-for-approximately-23-hours-on-usegalaxy-org/18516/1 "2026-10-20T14:11:17Z")

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Hello Galaxy support team,

My HISAT2 RNA-seq alignment jobs on [usegalaxy.org](http://usegalaxy.org) have remained gray for approximately 23 hours without starting. Could you please check whether this is a scheduling issue or if any action is needed on my side?

Details:

- Server: [https://usegalaxy.org](https://usegalaxy.org)
- History name: re try
- Tool: HISAT2 2.2.3+galaxy0
- Input: a collection of 6 paired-end samples, using completed fastp output (collection 26).
- Reference genome: built-in hg38 index.
- Output collection: 53, HISAT2 on collection 26: aligned reads (BAM).
- Example output dataset 54 was created on October 17, 2026 at 14:17:10 UTC+8 (06:17:10 UTC).
- The collection has 0 completed outputs. The example dataset page displays queued, while Job Information shows Job State: new.
- Standard output and standard error are empty; no exit code or job metrics are available.
- Storage usage is 251.9 GB of 268.4 GB (93%); I do not see a quota-exceeded or paused message.

Is the current wait expected, or are these jobs stuck before dispatch? Please also let me know if the remaining storage could prevent them from starting.

Thank you for your help!

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<div class="post-metadata">

**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:** [October 22, 2026, 12:25am UTC](https://help.galaxyproject.org/t/hisat2-jobs-remain-gray-new-for-approximately-23-hours-on-usegalaxy-org/18516/2 "2026-10-22T00:25:51Z")

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> [@Jobs stuck in "queued" state for hours on usegalaxy.org (Filtlong and Seqtk seq)](https://help.galaxyproject.org/t/jobs-stuck-in-queued-state-for-hours-on-usegalaxy-org-filtlong-and-seqtk-seq/18488/4):
>
> For the #queued-gray-datasets , there isn’t anything special happening at [UseGalaxy.org](http://UseGalaxy.org) right now. The usual advice about confirming your inputs and leaving queued work queued will apply.
> 
> Then, for [UseGalaxy.eu](http://UseGalaxy.eu) that is the same, and there is a dashboard where the exact status can be reviewed. → [How to see the UseGalaxy.eu job queue statistics](https://help.galaxyproject.org/t/how-to-see-the-usegalaxy-eu-job-queue-statistics/11837) with examples at [Search results for 'job statistics' - Galaxy Community Help](https://help.galaxyproject.org/search?q=job%20statistics) . All public Galaxy servers will look about the same.
> 
> * * *
> 
> Status: a few hours is still a very short queue! If work is queued longer than a day, then we can help with a review here.
> 
> - 🛠 The inputs, tool, parameters, and server can all matter for this. How to share your work with all of these details is in the banner topic, also here. → [FAQ: Sharing your History](https://training.galaxyproject.org/training-material/faqs/galaxy/histories_sharing.html)
> 
> To avoid delays later on…
> 
> - ⚙ [Workflows](https://help.galaxyproject.org/search?q=workflows) remain the best way to process batches of work. Most tutorials include [reusable workflow templates](https://training.galaxyproject.org/training-material/workflows/list.html). Once oriented, explore the [IWC Workflow Library](https://iwc.galaxyproject.org/) and try a **production workflow** for [streamlined batch analysis](https://iwc.galaxyproject.org/).
> 
> Please let us know how this work turned out or if you would like a closer look! 🙂

This advice will apply to you as well @linhhmo

Well, mostly. Alignment and assembly jobs can queue for a bit longer. Be sure to leave your work queued so you do not lose your place! If you want to share back your work, we can help you to make sure nothing more is going on.

Thanks! 🙂