# My sample for MarkDuplicates is not running

**URL:** <https://help.galaxyproject.org/t/my-sample-for-markduplicates-is-not-running/17507>\
**Category:** Uncategorized\
**Tags:** queued-gray-datasets\
**Created:** [February 26, 2026, 7:26am UTC](https://help.galaxyproject.org/t/my-sample-for-markduplicates-is-not-running/17507 "2026-02-26T07:26:37Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Bamgeut13](https://avatars.discourse-cdn.com/v4/letter/b/9de053/32.png) [@Bamgeut13](https://help.galaxyproject.org/u/Bamgeut13)\
**Post date:** [February 26, 2026, 7:26am UTC](https://help.galaxyproject.org/t/my-sample-for-markduplicates-is-not-running/17507/1 "2026-02-26T07:26:37Z")

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Hi, I am a beginner in run Galaxy. I’m trying to run my sample using MarkDuplicates and it has been more than 7 hours but it still says “this job is waiting to run”. Anyone can tell me what I can do? I appreciate your help. Thank you so much

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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 26, 2026, 9:04pm UTC](https://help.galaxyproject.org/t/my-sample-for-markduplicates-is-not-running/17507/2 "2026-02-26T21:04:41Z")

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Welcome @Bamgeut13

Your job is queued. This means the server where you are working is busy running other jobs. When those complete, your job will run!

We have many discussions here about how this works! See #queued-gray-datasets and this short guide 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).

* * *

* * *

**MarkDuplicates** jobs are big jobs! The `bam` is unpacked and all of the hit coordinates are compared to each other. Sometimes these will fail for a resource reason (running out of memory). The solution for a faster run is to make sure that you filtered your `bam` data first. This eases potential technical (resource) issues but it is also really important for scientific reasons.

> [@This job was terminated because it used more memory than it was allocated](https://help.galaxyproject.org/t/this-job-was-terminated-because-it-used-more-memory-than-it-was-allocated/13008/2):
>
> You can try to reduce the size of the BAM dataset through filtering out any reads that wouldn’t be used in the core analysis anyway. Meaning: removing unmapped reads, filtering by a minimum mapQ value (\>=20 or a strict \>=30) or filtering by the paired alignment state (proper pairs) or primary alignments or all combined!. Search the tool panel with “filter bam” for tool choices if you want to try this, and the extra step can be added to a workflow.

One other possibility is that there is a problem with the inputs for this job. Are these completed? Are they in a successful state (green color)? You could review the entire job on the [**Job Information Details**](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html) view for any of the output datasets to double check.

If you need help with this, you are welcome to consider [**Sharing your History**](https://training.galaxyproject.org/training-material/faqs/galaxy/histories_sharing.html) or posting screenshots that explain what is going on. The server and version of the tool may matter, so if you are just posting screenshots please make sure to capture all the details!

Please let us know if this helps or if you would like us to explore your work closer! 🙂