[question] limit memory kraken2

[egenomics]

Hi,
I am trying to run kraken2 on a machine with 50Gb RAM.

bactopia -profile singularity --wf kraken2 \
  --bactopia /home/jlvillanueva/Documents/SALMONELLA/bactopia_v3_results \
  --kraken2_db /home/jlvillanueva/bactopia/kraken_db/k2_pluspf_20221209.tar.gz \
  --include includes.txt --max_cpus 4 \
  -qs 2 \
  --max_memory 16

However my system crashes as it tries to use more memory than specified as you can see in this screenshot. Am I doing something wrong? Can kraken2 be limited by another means?

Thanks in advance.

[rpetit3]

You were correct in using --max_memory 16. I know with Docker, Nextflow will make sure the job doesn't go over 16 gb.

Let me see if it does the same for Singularity.

[egenomics]

It doesn't, in the screenshot you can see that is using more than 16Gb per job and crashes.

[rpetit3]

Did you also test with Docker?

[egenomics]

No, we can't use docker at the hospital for several internal reasons.

[rpetit3]

Good to know, I was aware of Docker sticking to the asked resource allocation (it kills jobs if memory is exceeded). I had only assumed Singularity did the same. Thank you for the info