Question: time to run cufflinks
gravatar for tkirkland
18 months ago by
tkirkland0 wrote:

How long does it take to run cufflinks? It has been submitted for 48 hours and still has the gray color with the !.

rna-seq • 577 views
ADD COMMENTlink modified 18 months ago by Jennifer Hillman Jackson25k • written 18 months ago by tkirkland0

Are you running the job at If so, how many queued jobs?

ADD REPLYlink written 18 months ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
18 months ago by
United States
Jennifer Hillman Jackson25k wrote:


I found your history. The input Tophat BAM datasets require that the metadata be reset before downstream tools can execute. Do this by clicking on the "reset metadata" link in the yellow alert box inside the expanded dataset or by clicking on the dataset's pencil icon to "detect metadata" using the Edit Attributes forms.

We realize this is inconvenient when running workflows and are now recommending that HISAT be used going forward instead of Tophat. Tophat is outdated software and will be soon deprecated at That will very likely occur this week or early next.

Thanks and our apologies for the current problems with this tool.

Jen, Galaxy team

ADD COMMENTlink written 18 months ago by Jennifer Hillman Jackson25k
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