Question: Jobs starting to run and then stopping
0
gravatar for cmarcho
3.3 years ago by
cmarcho10
Greece
cmarcho10 wrote:

Hi,

Recently I have been using Galaxy to run Cufflinks but I have been having problems where a job will sit waiting to run for a long time (over 12 hours), then will go yellow and start to run, and then go grey and stop running. When it stops running, it ends up sitting for days. I have tried restarting the run, but it does the same thing. It starts, then stops and says it is waiting to run. 

Is anyone else having this problem and is there anything I can do to fix this? Runs that I did 2 weeks ago worked fine...

Thanks!

Chelsea

rna-seq galaxy cufflinks speed • 925 views
ADD COMMENTlink modified 3.3 years ago by Jennifer Hillman Jackson25k • written 3.3 years ago by cmarcho10

Just a note, a job that was running just reverted back to "waiting" status. 

ADD REPLYlink written 3.3 years ago by cmarcho10

Was this the first time it was reverted? If so, then that is expected as it moves to the other cluster. If it has bounced that twice, then we would like to examine this in more detail as it is not expected.

ADD REPLYlink written 3.3 years ago by Jennifer Hillman Jackson25k

Everything only gets reverted once that I can tell, so it should be the case that you described below.

ADD REPLYlink written 3.3 years ago by cmarcho10
2
gravatar for Jennifer Hillman Jackson
3.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The job almost certainly exceeded the "wall-time" of the first cluster, then was sent to the second, as described here:
https://wiki.galaxyproject.org/Main#Job_resubmission_to_Stampede

If the job fails after that, then it is too large to execute on http://usegalaxy.org. Other choices are:
https://wiki.galaxyproject.org/Support#Job_failure_reason_.22ran_longer_than_the_maximum_allowed_job_run_time.22

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.3 years ago by Jennifer Hillman Jackson25k

Thanks for your reply, these are some of the bigger files that I have tried to run so that makes sense. I wasn't aware of the wall-time/resubmission thing, so thanks for that information!

ADD REPLYlink written 3.3 years ago by cmarcho10
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