I am encountering a problem similar to that mentioned here: https://www.biostars.org/p/45848/
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.