Tophat2 "Joining Segment Hits" Does Not Complete

Question

[David Langenberger]

Tophat2 runs nicely (6 hours) up to the step "joining segment hits". But this step (single core process, named longspanningreads") is running now for almost one week.

• data: 454-sequencing reads up to 500 nucleotides long probably containing a lot of exon-exon junctions.
• Tophat version 2.0.0
• Bowtie version: 2.0.0.6

here is the command:

tophat2 -p 12 -o tophat_out genome 454_data.fastq.gz

Does anyone has an idea what could cause this? Or maybe someone knows which parameter can be adjusted to reduce the time for this step.

Thanks

Answer 1

[Rohit]

I think you must have been using Tophat for other samples or at different parameters parallely. The program must have got stuck. It does not usually run for such a long time.

Why don't you check the run and log-file. Check the pmap id for the process in Linux too to be sure if you want to force close it.

Answer 2

[David Langenberger]

Hi Rohit, thanks for answering!

There were no other jobs running besides this tophat job. What I realized: Tophat2 runs nicely (6 hours) up to the step "joining segment hits". But this step (single core process, named "longspanningreads") runs then forever and ever and ever and.....

Unfortunately I do not have the log file any more (4 month ago...), but I remember that there were no specific error messages.

[Rohit]

Actually its wierd that the command ""tophat2 -p 12 -o tophatout genome 454data.fastq.gz"" worked.

As far as I have used, it goes as ""tophat -p 12 -o tophatout genome 454data.fastq.gz"" Without the "2"

[John Torcivia]

When tophat2 is installed, tophat is replaced with a symlink (or maybe a python wrapper - I can't remember) to tophat2 in the /usr/bin directory (or wherever installed). So in reality when you run tophat you're getting tophat2 unless you have a really old version I guess.