Question: Long wait times Htseq, featurecounts and Cufflinks
gravatar for TJ
17 months ago by
TJ0 wrote:

Hi I have tried running a few jobs (~15) on Cufflinks, feature counts and Ht-seq counts. While a few of the jobs were done within an hour, the remaining jobs have been waiting to run for more than 2 days.

Is there a way for me to speed up this process?

Best and thanks TJ

EDIT: I use the main Galaxy server @

rna-seq galaxy cufflinks • 503 views
ADD COMMENTlink modified 17 months ago by Jennifer Hillman Jackson25k • written 17 months ago by TJ0
gravatar for Jennifer Hillman Jackson
17 months ago by
United States
Jennifer Hillman Jackson25k wrote:


This is a normal wait time after starting up so many jobs at once.

Logic: A batch of your jobs will go through, then others that haven't run jobs today will get a batch of their's through, then you will get a batch through, repeat. This helps to share resources fairly among all users. Some people queue up many jobs at time, others just one or two. Each get a "batch" through on each rotation. Deleting/restarting jobs in your account will not change this, except to place the new jobs at the back of the queue, extending wait time even more.

If no jobs at all run within your account, across all of your histories, in any 24-36 hour time period, please let us know. That indicates a problem.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 17 months ago by Jennifer Hillman Jackson25k
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