Question: Jobs running for over 24 hours ( still unfinished) that previously took a few hours?
gravatar for a.morris
13 months ago by
a.morris40 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
ADD COMMENTlink modified 13 months ago by Jennifer Hillman Jackson25k • written 13 months ago by a.morris40
gravatar for Jennifer Hillman Jackson
13 months ago by
United States
Jennifer Hillman Jackson25k wrote:


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, please include where and we can follow up from there.

Thanks, Jen, Galaxy

ADD COMMENTlink written 13 months ago by Jennifer Hillman Jackson25k

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:

Try using HISAT2 instead. Tophat is considered deprecated.

RNA-seq tutorials that demonstrate HISAT2 usage:

ADD REPLYlink written 13 months ago by Jennifer Hillman Jackson25k
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