Galaxy jobs starting and then returning to grey and not running...

Question: Galaxy jobs starting and then returning to grey and not running...

3.5 years ago by

United Kingdom

Hi,

I've recently had issues with tophat running (and some other jobs) on the public Galaxy server. Initially they start as normal and go yellow, however, when I come back they have gone back to grey and then never seem to run. Has anyone else encountered this issue/know how to fix it? I am at ~50% storage capacity so that is not the issue...

Best,

Jonathan

tophat galaxy • 786 views

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modified 3.5 years ago by ramyak1912 • 0 • written 3.5 years ago by jonathanneve89 • 0

3.5 years ago by

jling • 70

United States

jling • 70 wrote:

https://wiki.galaxyproject.org/Main#Job_resubmission_to_Stampede

There are time limits now for each program before they are resubmitted to the TACC supercluster

I wish they would increase the time limits (especially for tophat, since 6hrs is really not good enough for modern day RNA-seq that generally has 50-80million reads)

ADD COMMENT • link written 3.5 years ago by jling • 70

3.5 years ago by

ramyak1912 • 0

United States

ramyak1912 • 0 wrote:

Yes I have noticed that too. I have paired end data and I am trying to run tophat and the job never runs completely. I didnt know there are time limits now. Do you know any other way I can do this?

Thanks !

ADD COMMENT • link written 3.5 years ago by ramyak1912 • 0

No, you can save a little time by setting the Job Resource Parameter as TACC Stampede to have it enter the queue right away but I think that's it

ADD REPLY • link written 3.5 years ago by jling • 70

Thanks for this info. Is this queue usually quite long as I have tried this before but using this computing resource it never seems to move off queued.

ADD REPLY • link written 3.5 years ago by jonathanneve89 • 0

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