Question: TopHat is waiting to run more than 24h
1
gravatar for jjv.bioinformatics
4 months ago by
jjv.bioinformatics10 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?

rna-seq • 208 views
ADD COMMENTlink modified 4 months ago by Jennifer Hillman Jackson22k • written 4 months ago by jjv.bioinformatics10
1

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

ADD REPLYlink modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson22k

Then, those which are queued (waiting to run), do I have to reload or to wait ?

ADD REPLYlink written 4 months ago by jjv.bioinformatics10

Wait - these should queue up today. If not, please write back and let us know.

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson22k

Still They are waiting to run, is it normal or have I any problem?

ADD REPLYlink written 4 months ago by jjv.bioinformatics10
1

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

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson22k

Still They are waiting to run, is it normal or have I any problem?

ADD REPLYlink written 4 months ago by jjv.bioinformatics10

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

ADD REPLYlink written 4 months ago by bioraihan40
0
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson22k wrote:

Update for job delays and/or cluster failures at http://usegalaxy.org 5-22-2017: https://biostar.usegalaxy.org/p/23219/#23225

ADD COMMENTlink written 4 months ago by Jennifer Hillman Jackson22k
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