cufflinks-0.9.1 Hangs

[peromhc]

Hi All,

Using the new verison of TopHat, then the new version of Cufflinks here..

The program stalls/hangs at 13% complete- multiple times now..

The command:

/home/macmanes/cufflinks-0.9.1/cufflinks -N -r /media/hd_/tophat-1.1/social/tophat_out/tucomrna.fa --num-importance-samples 5000 --max-mle-iterations 20000 -p 15 /media/hd_/tophat-1.1/solitary/tophat_out/accepted_hits.bam

Screen output:

[20:13:29] Inspecting reads and determining fragment length distribution.
> Processing Locus 253055:2-223                [***                      ]  13%

Any idea why it is hanging? Sat like this (13%) for 12 hours today..

[adarob]

Would you be willing to make this dataset available so I could try to find out what's happening?

-Adam
[email protected]

[joro]

Was there a solution to this?
I ran cufflinks 0.9.3 yesterday and although it says 100%, cufflinks still seems to be running:

[16:08:03] Assembling transcripts and estimating abundances.
> Processing Locus X:124110855-124110905     [*************************] 100%

Thanks in advance for any suggestions.

[joro]

The SAM file is 21G

[adarob]

@joro,

Can you try running with verbose processing (-v) and post the last few lines before it hangs?