Question: TopHat is waiting to run more than 24h
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jjv.bioinformatics • 10 wrote:
I put a TopHat 24 hours ago and still it is waiting to run. I have been reading that it´s possible to be in a queue but if I execute other programs, such as FastQC, Groommer, They run as fast I click them. I can´t understand why. Do I have to wait more time or something is wrong?
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modified 18 months ago
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Jennifer Hillman Jackson ♦ 25k
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18 months ago by
jjv.bioinformatics • 10
Hello,
There was a cluster issue over the weekend that is now resolved.
If any jobs failed, please rerun them. Those that are queued should be left queued until they begin to execute.
Our apologies for the problem and thanks to you and others for reporting the issue!
Jen, Galaxy team
Then, those which are queued (waiting to run), do I have to reload or to wait ?
Wait - these should queue up today. If not, please write back and let us know.
Still They are waiting to run, is it normal or have I any problem?
Update:
Thanks for reporting the issues. The admins at http://usegalaxy.org are investigating. More feedback soon. Meanwhile, avoiding the Jetstream cluster is one potential workaround as we think this is where the current problem is localized.
How to set job resources: https://galaxyproject.org/main/#choosing-computational-resources
Pick one of the first two in the list. Avoid leaving this at default as this does not mean the job goes to the "Default" cluster in the list (sometimes referred to as "Roundup") but rather to any of the three primary production clusters based on load. "Default" resources does exclude the test clusters, which are unpredictable as they are actually used for testing and are not recommended even when specified (jobs can fail for many reasons on those).
Jen, Galaxy team
Still They are waiting to run, is it normal or have I any problem?
I am having the same issue. Its been couple of days now. I tried rerun them couple of times in a interval of 12h but I still have the same issue. Regards, Raihan