Cuffdiff 2 progress reporting

[barkasn]

Hi All,

I am running cuffdiff2 on 2 samples with 4 replicates each and a total of 160m reads (PE 80bp) for nearly 48 hours now, however I don't get any feedback about progress and I have no way of determining if this is normal operation or if cuffdiff is stuck.

The program is using 100% of 1 CPU and 0% memory (despite specifying -p 7) and the only output so far has been "You are using Cufflinks v2.1.1, which is the most recent release." on stderr. A number of files have been created in the output directory but they are all empty.

Is this normal for this version of cuffdiff? What are your experiences?

Thanks in advance,

barkasn

[TiborNagy]

It is absolutly normal if you do not have free disk space :-)

[barkasn]

The issue had to do with the script calling cuffdiff, it would provide the path to the samfiles but not the actual name. Cuffdiff did not display an error message and kept on running using a single processor. This is a bug really and should be fixed.