Question: cufflinks running problem
gravatar for francesca.paieri
21 months ago by
francesca.paieri0 wrote:


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,


rna-seq cufflinks • 517 views
ADD COMMENTlink modified 21 months ago by Jennifer Hillman Jackson25k • written 21 months ago by francesca.paieri0
gravatar for mrals
21 months ago by
mrals0 wrote:

Hmm, did you look at the standard output and standard error? Sounds like a server issue.

ADD COMMENTlink written 21 months ago by mrals0
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson25k wrote:


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

If working at (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 COMMENTlink written 21 months ago by Jennifer Hillman Jackson25k
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