Cuffldiff is almost done, but it seems to be hanging at "99% complete"

Question

[M K]

I'm trying to calculate gene expression. Cuffldiff is almost done, but it seems to be hanging at "99% complete". What's going on?

Answer 1

[Ashutosh Pandey]

From Cufflinks FAQ I found this:

I'm trying to assemble a sample. Cufflinks is almost done, but it seems to be hanging at "99% complete". What's going on?

Cufflinks spawns threads for each locus to assemble and quantitate the "bundle" of reads in that locus. Some loci may have more reads and more complicated alternative splicing than others, which requires more CPU cycles. These bundles can continue processing long after all others have completed, leading to this behavior. You may be able to decrease the number of such bundles by masking out ribosomal and mitochondrial RNA using the -M/--mask-file option described in the Manual.

Answer 2

[laboiss]

M K, have you had any luck? Other threads I've looked at said the masking option didn't resolve the issue, so I'm wondering if you were able to figure out what went wrong? I'm having the same problem on two separate projects, they're both stuck at 99% for multiple days now. I'd appreciate and advice!

Thanks