Question: Cufflink not running
gravatar for yokabarrathi287
7 months ago by
yokabarrathi2870 wrote:

Dear galaxy admin and user,

Cufflink is not running for two particular datasets. While cufflink for other datasets have been done. Even upon rerunning the job, cufflink process doesn't start. I get this following message upon clicking the cufflink file "This is a new dataset and not all of its data are available yet". What is the real meaning of this? Should I run this job again?

any suggestion, how to proceed

ADD COMMENTlink modified 7 months ago by Jennifer Hillman Jackson25k • written 7 months ago by yokabarrathi2870
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Jobs can queue and execute at different rates. When running multiple large jobs (Cufflinks is considered large), some will start, complete, then others will run. Resources are shared among all users of the public Galaxy Main server.

A gray job indicates that it is queued. Avoid deleting and restarting, as this removes the original job from the queue and places the new one back at the end, further extending wait time.

Support FAQs that describe how jobs execute:

More details about Galaxy Main and jobs/resources:

The only reason why a job would stay queued and never run is if one of these is going on:

  1. There is a server/cluster problem. Those can be reported here. None are known right now, and if your other jobs are running, a problem server-side is very unlikely to be a factor.

  2. One or more of the inputs to the job are in an error state. Check to make sure these are active datasets (not deleted) and are intact (no metadata warnings). This includes the BAM input plus any reference annotation GTF or custom reference genome used.

  3. If your account is over quota (250 GB), a warning will be shown above the history panel stating that new jobs cannot be run until you are back under quota. The solution is to permanently delete unneeded data. Download a backup first if you wish to use it again later.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 7 months ago • written 7 months ago by Jennifer Hillman Jackson25k

I checked your account the problem is that the input Tophat jobs are in a metadata error state (item 2 above). Dataset 135 is an example. There were no hits. Double check that the sequences are human (since you are mapping against hg38), consider doing some QA on the fastq data, and then using HISAT2 instead (Tophat is considered deprecated). Your other mapping jobs might also need to be rerun, after doing fastq QA, to try to capture more hits, or if you decide to use HISAT2 instead.

Example workflows for QA and RNA-seq are in the Galaxy tutorials here:

ADD REPLYlink modified 7 months ago • written 7 months ago by Jennifer Hillman Jackson25k
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