How to enable multiple cores/threads for Bowtie2 or BWA using Macbook M2 chip?

Question

[weixiaokuan]

Dear Community,

I am trying to use bowtie2 or bwa multi-core/threads option to align my reads to genome (-p 4). I am using a MacBook pro m2 chip and it seems cannot fully parallelly use all the cores. using 'top", it shows 4/1 for threads (#TH) and only one process for bowtie2. Could someone clarify this? and let me know how to enable parallel multi-threads for using these aligners on Mac M2 chips? Thank you!

-Xiaokuan

Answer 1

[GenoMax]

Programs do not use all the threads/cores all the time. They will do so during appropriate part of the analysis. As long as you have enabled use of multiple threads on your command line there is nothing else you need to do.

[weixiaokuan]

Thank you for your answer @GenoMax!

Is there a way to dynamically monitor threads usage for a specific command such as bowtie2? I previously assumed that "top" command might show such information but it seems not effective.

Thank you!

[GenoMax]

top will show thread info but it will be aggregated in % (e.g. you will see 400% use for 4 cores). You could use htop to look at individual cores. Looks for directions to install on net.