How to set the number of threads

[SchulzLab]

Hi, I am running bs3-align.py and I am wondering if one can set the number of threads to use? Currently it seems that 2 SNAP threads are running. I could not find an option in the readme or option output of bs3-align.py.

Thanks for the help, Marcel

[sbaheti]

you can pass in -t option using --snap- to specify threads. i have not tried it myself yet.

[supermaxiste]

Hi, I actually tried to use the -t option with bs-align and not only it didn't work, but it kept using all the 32 cores of the server I was working on. After a look at the bs-align code I found out that the -t option is hardcoded in line 263 (single-end) and 413 (paired end). If you would like to change the number of threads you need to modify those numbers. Just for clarity, here's how line 263 looks:

aligner_command = './snap single %(reference_genome)s -fastq %(input_file)s -o -sam %(output_file)s -h 630 -d 20 -t 32 -b' + aligner_options_string()

If you would like to limit at 10 threads, you should modify as follows:

aligner_command = './snap single %(reference_genome)s -fastq %(input_file)s -o -sam %(output_file)s -h 630 -d 20 -t 10 -b' + aligner_options_string()

Hope that helps!