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Question: cufflinks running problem
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gravatar for francesca.paieri
21 months ago by
francesca.paieri • 0
francesca.paieri • 0 wrote:

Hello,

I´m having problems in running Cufflinks. Yesterday morning I used the Tophat accepted hits of my 6 samples, to run cufflinks. Untill today just one cufflinks worked, the rest of the jobs are still grey"This is a new dataset and not all of its data are available yet". All the Tophat run in parallel and with the same reference genome.

How can I solve this problem? What does it mean when it get stuck like this?

Thanks a lot,

Francesca
rna-seq cufflinks • 517 views
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modified 21 months ago by Jennifer Hillman Jackson ♦ 25k • written 21 months ago by francesca.paieri • 0
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gravatar for mrals
21 months ago by
mrals • 0
mrals • 0 wrote:

Hmm, did you look at the standard output and standard error? Sounds like a server issue.
ADD COMMENT • link written 21 months ago by mrals • 0
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gravatar for Jennifer Hillman Jackson
21 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The jobs are queued and should be allowed to stay in the queue until processed.

If working at http://usegalaxy.org (and many other public/local servers), jobs will execute out of the queue when there are cluster resources available.

That said, if the inputs for a job are not ready to use, then this can also cause a job to stay queued until they are ready. Tophat jobs that are still running are one scenario, but also double check any completed input tophat jobs to make sure there are no metadata corrections needed (certain Tophat jobs end this way right now, a known issue). If your Tophat jobs do need the metadata auto-detected, do that with the provided links and then restart the Cufflinks jobs (you will not be able to adjust metadata while the dataset is used as input to another tool - queued or executing).

Thanks, Jen, Galaxy team
ADD COMMENT • link written 21 months ago by Jennifer Hillman Jackson ♦ 25k
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