Salmon Jobs Stuck in Queue for Over Two Days – Galaxy US

[sfathim]

I submitted 24 paired-end RNA-seq samples for Salmon quantification on Galaxy US over two days ago, but none of the jobs has started running. They are all still showing a “new/queued” status, with no error messages.

I also submitted a GFFread job, which has been stuck in the queue.

I tested Salmon with one of the same samples on Galaxy Europe, and the job completed successfully.

Could you please let me know if there is an issue with the Galaxy US job queue or if there is anything I should do to get my jobs running?

Thank you so much for your help!

[jennaj]

@jennaj

For the queued-gray-datasets , there isn’t anything special happening at UseGalaxy.org right now. The usual advice about confirming your inputs and leaving queued work queued will apply.

Then, for 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 with examples at Search results for 'job statistics' - Galaxy Community Help . All public Galaxy servers will look about the same.

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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

To avoid delays later on…

• Workflows remain the best way to process batches of work. Most tutorials include reusable workflow templates. Once oriented, explore the IWC Workflow Library and try a production workflow for streamlined batch analysis.

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, @sfathim

The servers have different queues, so one may be “faster” than the other, overall or just for some tools, but they are each still processing tens of thousands of jobs everyday. Work will queue first, then execute, and this is expected.

Since yours has been a few days already, and because Salmon is such a complicated tool to use, would like like to share back your work for review? To make sure more is not going on? You can also review prior troubleshooting here Search results for 'salmon' - Galaxy Community Help but please ask for help if you are still stuck!

I’ll watch for your reply, thanks!