My sample for MarkDuplicates is not running

[Bamgeut13]

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

[jennaj]

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:

@jennaj

When working at UseGalaxy.org, UseGalaxy.eu, or UseGalaxy.org.au, your analysis jobs execute at large scale academic clusters. Hundreds of thousands of jobs process each month!

• Use a Workflow for batch work.
• Allow queued (grey color) and executing (yellow-orange) datasets 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 (especially for ‘big’ jobs, e.g. alignments).

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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.

@jennaj

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 view for any of the output datasets to double check.

If you need help with this, you are welcome to consider Sharing your History 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!