Question: Tophat with -p option freezes computer
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gravatar for jmack159
5.0 years ago by
jmack15920
United States
jmack15920 wrote:

I recently got a used/new workstation with two, quad-core Xeon processors, 8 GB RAM (for the time being), 240 SSD for system, and 1TB HDD for data. I installed biolinux 8 and tried to process some RNA-seq data (~18M reads) using tophat v2.0.9. The problem is that running with a decent size -p argument results in the computer completely freezing (keyboard, mouse, everything non-responsive). Watching the system monitor, I am not running out of RAM (also have a decent swap set aside on SSD), nor do I see any other indications I am running out of resources.

Running bowtie2 alone with -p 8 works fine, and I also tried titrating the -p value for tophat starting from 1.

-p 1 -> success
-p 2 -> success
-p 3 -> success
-p 4 -> computer freezes
-p 7 -> computer freezes
-p 8 -> computer freezes

The freeze always occurs during the following step:
Mapping left_kept_reads to genome genome with Bowtie2 

There is nothing in the system nor tophat logs to indicate there are any issues. Any idea what is causing my machine to freeze? 

rna-seq software error • 1.4k views
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