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Tophat2 "Joining Segment Hits" Does Not Complete

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

next-gen tophat2 split read mapping
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written by David Langenberger David Langenberger

2 answers

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.

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written by Rohit Rohit

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.

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written by David Langenberger David Langenberger

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"

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written by Rohit Rohit

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.

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written by John Torcivia • John Torcivia

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