> 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


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,
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