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?