Question: Galaxy jobs starting and then returning to grey and not running...
0
gravatar for jonathanneve89
3.5 years ago by
United Kingdom
jonathanneve890 wrote:

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
ADD COMMENTlink modified 3.5 years ago by ramyak19120 • written 3.5 years ago by jonathanneve890
1
gravatar for jling
3.5 years ago by
jling70
United States
jling70 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 COMMENTlink written 3.5 years ago by jling70
0
gravatar for ramyak1912
3.5 years ago by
ramyak19120
United States
ramyak19120 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 COMMENTlink written 3.5 years ago by ramyak19120

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 REPLYlink written 3.5 years ago by jling70

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 REPLYlink written 3.5 years ago by jonathanneve890
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 175 users visited in the last hour