Question: Jobs running for over 24 hours ( still unfinished) that previously took a few hours?
0
gravatar for a.morris
6 weeks ago by
a.morris10
a.morris10 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 • 128 views
ADD COMMENTlink modified 6 weeks ago by Jennifer Hillman Jackson23k • written 6 weeks ago by a.morris10
0
gravatar for Jennifer Hillman Jackson
6 weeks ago by
United States
Jennifer Hillman Jackson23k 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 COMMENTlink written 6 weeks ago by Jennifer Hillman Jackson23k

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 REPLYlink written 6 weeks ago by Jennifer Hillman Jackson23k
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