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Question: TopHat, Cufflinks, and CuffDiff jobs still querying
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gravatar for asshah
2.6 years ago by
asshah • 0
asshah • 0 wrote:

I'm having issues running TopHat, Cufflinks, and Cuffdiff. The jobs stay grey (with exclamation points) for an astronomical amount of time. Is this normal? I've run all of these RNA-seq tools before and they run in a reasonable amount of time. Could this be an issue with the main galaxy server? If so how quickly will changes be made. I have a final project due for a class in the next 5 days and I need my outputs fairly soon.

Thank you for all the help.
rna-seq tophat software error cufflinks • 743 views
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modified 2.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.6 years ago by asshah • 0

UPDATE: Getting an error after some time that says the following "An error occurred while getting updates from the server. Please contact a Galaxy administrator if the problem persists"

ADD REPLY • link written 2.6 years ago by asshah • 0
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gravatar for Jennifer Hillman Jackson
2.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

We believe that a few jobs may have a deployment problem to the cluster. So, even though in most cases we state to wait for queued jobs to execute for best performance - in this specific case, at this specific time, deleting the job and re-running is the recommendation.

For others reading - if jobs have been queued for longer than 10 hours, and your account does not have other jobs already running, please do the same.

For the pop-up warning - that just means the server is busy. It should clear up if it hasn't already.

Our apologies for the confusion during this upgrade phase at http://usegalaxy.org.

Thanks, Jen, Galaxy team
ADD COMMENT • link modified 2.6 years ago • written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

Update, please see: A: Jobs caught in long term grey zone (!)

ADD REPLY • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k
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