A way to limit the amount of memory that sortmerna uses during alignment?

[jackieway]

Hello, I am running sortmerna version 4.3.6 on a machine with 256 GB of RAM and 128 threads. I am running a sample with 124 M paired end reads, and have set my WSL2 configuration to use all of the available RAM. I'm receiving an out of memory error and the process gets killed part of the way through alignment, and sortmerna in general is working (ran successfully on a sample with 56 M paired end reads). I saw that there is a flag -m that allows the user to adjust the amount of memory used for index building, but the process is killed through alignment. Is there any way I can cap the memory used by sortmerna so that I can use it on my sample?

[biocodz]

Sortmerna doesn't have a built-in resource management, but you can use system facilities like cgroups for that. WSL can also exacerbate the problem, so I avoid it for this reason.
We might consider this as a feature for the future development.