Starting Call Set Refinement (CSR) filtering provokes RAM overload about octopus HOT 2 OPEN

Hi,

I'm currently having similar issues with Octopus processing human whole genomes (30x) using the docker image and singularity. Octopus runs well until the Call Set Refinement filtering is started, after which it is killed by an oom leak. I haven't been able to figure out yet how to solve this. I have tried multiple configurations, adjusting the maximum RAM memory (up to 250Gb, 12Gb per core) without any success. Any ideas?

Version
octopus 0.7.4
docker image pulled from: https://hub.docker.com/r/dancooke/octopus

Command
singularity run --nv
--bind /path/to/bamfiles//mnt/bamfiles,
/path/to/ref:/mnt/ref,
/path/to/output:/mnt/output,
/path/to/singularity/image
-R /mnt/ref/Homo_sapiens_assembly38.fasta
-I /mnt/bamfiles/${bamName}
-T chr1 to chrX
--sequence-error-model PCRF.HISEQ-2500
--forest-model /mnt/bamfiles/germline.v0.7.4.forest.gz
-o /mnt/output/${bamNameWithoutExtension}.vcf.gz
--threads $threads

Thanks in advance for your time!
Kind regards
Sven

from octopus.

In the past, I have only run octopus on 30x WGS human with something like 1900G RAM, but I did not look at the peak RAM usage. I would recommend you split your job into parts, and maybe try again per chromosome. Do you really have the forest model file? That is something that could also cause an error if you do not have it, but I am not sure if it would cause the same OOM error.

from octopus.