An error occurred running this job:cufflinks v1.0.3
cufflinks -q --no-update-check -I 1 -F 0.050000 -j 0.050000 -p 8 -g =
/galaxy/main_database/files/002/991/dataset_2991920.dat
Error running cufflinks. [bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this

Hello,

Without seeing your analysis, it's difficult to determine what the problem is. My best guess is that:

(a) your SAM/BAM dataset is not compatible with Cufflinks for some reason, perhaps due to sorting?
(b) your gene annotation dataset is not compatible with Cufflinks.

Perhaps looking at the Cufflinks documentation will help you determine the error: http://cufflinks.cbcb.umd.edu/

If that doesn't work, you can report the problem by clicking on the bug icon next to the failed datasets.

Good luck,
J.