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?
