Question: Cufflinks output empty
gravatar for gupta
6 months ago by
gupta20 wrote:


I am encountering a problem similar to that mentioned here:

I am on the main Galaxy server. I have 6 samples, and Cufflinks worked fine for 4 samples. The other two samples return an 'empty output'. I am running Cufflinks without any input annotation file and using the exact same workflow for all samples.

In general, job execution is taking extremely long (> a day for a single submission).

Can someone please help me resolve this issue? Thanks in advance.

Best, PG

cufflinks galaxy main • 124 views
ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson23k • written 6 months ago by gupta20
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson23k wrote:


The job may be failing due to the size exceeding the memory or other cluster resources available at However, I would suggest one more rerun given the recent server issues.

Please see here for server updates and links to troubleshooting help for failed job troubleshooting and alternative ways to use Galaxy for very large jobs:

Thank you for reporting the problem! Jen, Galaxy team

ADD COMMENTlink written 6 months ago by Jennifer Hillman Jackson23k
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