Hello, due to some limitations, I could only run nf-core/atacseq on a MacBook with 8 cores and 8 GB of memory. I added

-profile arm

to my command and nextflow.config in my working directory:

process {
  resourceLimits = [
    cpus: 8,
    memory: 8.GB
  ]
}

Everything worked well until SAMTOOLS_SORT, where I kept encountering error exit status (137), so I assume there was still an out of memory issue. (Also tried adding

--max_memory 8GB

to my command but didn't work as well.) Is there any chance I could bypass this error? Thank you.

Hi! I am afraid that you will need more memory to analyse your data set sad cowboy

You could try lowering the number of cpus for samtools/sort and/or specifying

-m

in the command The documentation says it uses 768MB per thread by default.

Thank you very much! Is there a way in the command to specify

-m

for samtools? Sorry that I'm pretty new to nextflow syntax.

I am afraid that currently only fastq files are accepted

Got it. Thank you!

Thank you very much! Is there a way in the command to specify

-m

for samtools? Sorry that I'm pretty new to nextflow syntax.

Take a look at this: https://nf-co.re/docs/usage/getting_started/configuration#customising-tool-arguments

Thank you, I'll give it a try!