# Job seems stuck for RNA STAR

**URL:** <https://help.galaxyproject.org/t/job-seems-stuck-for-rna-star/16582>\
**Category:** usegalaxy.org support\
**Tags:** queued-gray-datasets\
**Created:** [December 18, 2025, 3:09am UTC](https://help.galaxyproject.org/t/job-seems-stuck-for-rna-star/16582 "2025-12-18T03:09:33Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![apeinasuit](https://avatars.discourse-cdn.com/v4/letter/a/57b2e6/32.png) [@apeinasuit](https://help.galaxyproject.org/u/apeinasuit)\
**Post date:** [December 18, 2025, 3:09am UTC](https://help.galaxyproject.org/t/job-seems-stuck-for-rna-star/16582/1 "2025-12-18T03:09:33Z")

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I have RNA Star jobs running for 24 pairs, 22 OK and 2 running, but this has been the case for 2 days. Is there an issue with the data or the server? What can I do?

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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:** [December 18, 2025, 6:48am UTC](https://help.galaxyproject.org/t/job-seems-stuck-for-rna-star/16582/2 "2025-12-18T06:48:58Z")

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Welcome @apeinasuit

It sounds like you just ran a larger batch of mapping jobs. Those will be split up between the clusters into smaller batches (automatically) but this might be difficult to visualize from the top level of the collection folder.

Some of those executed, then completed, then next set executed and completed, and now the last batch is still executing. Try to _leave those jobs executing_ to get the result!

Next time, you can consider using a workflow to speed things up. A workflow queues all the jobs in an analysis project at the same time. This means that the next tool can start to process for some samples, whenever they are ready, even while other samples are still completing that initial step. When there are many higher computation tools all run in a series, or when there are many samples, or both, this “streaming through tools” can considerably speed things up!

**In short:** my guess is that the jobs that are executing now were only queued before, not actually running, but as the other jobs completed, the last few jobs are now actually running. If this doesn’t clear up after a day or so, you are welcome to post back a link to the history and we can help to confirm that this is all proceeding as expected.

Hope this helps! 🙂

XRef →

For many more examples, please see #queued-gray-datasets

And, the general process is here:

> [@Troubleshooting resources for errors or unexpected results](https://help.galaxyproject.org/t/troubleshooting-resources-for-errors-or-unexpected-results/42/1):
>
> ⏰ When working at [UseGalaxy.org](http://UseGalaxy.org), [UseGalaxy.eu](http://UseGalaxy.eu), or [UseGalaxy.org.au](http://UseGalaxy.org.au), your analysis jobs execute [at large scale academic clusters](https://training.galaxyproject.org/training-material/faqs/galaxy/#analysis). Hundreds of thousands of jobs process each month!
> 
> - Use a [Workflow](https://training.galaxyproject.org/training-material/search2?query=workflow) for batch work.
> - Allow [queued (grey color) and executing (yellow-orange) datasets](https://training.galaxyproject.org/training-material/faqs/galaxy/datasets_job_status.html) to finish processing.
> - Deleting and rerunning puts your job back _at the end_ of the queue again!
> - Job priority is the exactly the same for everyone.
> - **Be patient**. Galaxy is a free service, when a lot of people are using it, [you may have to wait longer than usual](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_jobs_not_running.html) (especially for ‘big’ jobs, e.g. alignments).