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Question: Jobs running for over 24 hours ( still unfinished) that previously took a few hours?
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gravatar for a.morris
13 months ago by
a.morris • 40
a.morris • 40 wrote:

I have started to run Tophat twice for 4 datasets. Both attempts have resulted in the jobs still running 24 hours later. In the past such jobs took a few hours not over 24 hours. No error messages are shown
rna-seq galaxy • 424 views
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modified 13 months ago by Jennifer Hillman Jackson ♦ 25k • written 13 months ago by a.morris • 40
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gravatar for Jennifer Hillman Jackson
13 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Some queues get busy on weekends. I suspect that was the delay.

Let us know if these jobs have completed or if the state is still grey (queued, waiting to run) and/or now yellow (executing). If you are not working at https://usegalaxy.org, please include where and we can follow up from there.

Thanks, Jen, Galaxy
ADD COMMENT • link written 13 months ago by Jennifer Hillman Jackson ♦ 25k

I took a look at your histories and the jobs did complete, but some failed. The delays appear to be related to stopping/restarting a lot of jobs at once (this also takes up resources and can cause delays).

The failure reason has to do with a bug in the data tables for papham1. We'll try to get this fixed, has been around a while, impacts Bowtie2/Tophat2. Ticket: https://github.com/galaxyproject/galaxy/issues/3604

Try using HISAT2 instead. Tophat is considered deprecated.

RNA-seq tutorials that demonstrate HISAT2 usage: https://galaxyproject.org/learn/

ADD REPLY • link written 13 months ago by Jennifer Hillman Jackson ♦ 25k
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