run chromosight with --inter option on each interchromosome matrix separately about chromosight HOT 2 CLOSED

Hi @jazberna1,

Chromosight already loads only 1 sub matrix (per process) at a any time. So if you have 4 threads, you will have 4 inter/intra-chromosome matrix loaded in RAM at a given time. They are removed from memory as soon as they are processed.

If you want to reduce RAM usage, you can therefore use --threads=1, or use a lower resolution matrix. The latter should drastically reduce RAM usage (e.g. going from 10kb to 20kb). Higher coverage matrices also take more RAM.

For now, this is all we can do to reduce RAM usage. The only way to overcome this would be to tile chromosomal matrices and load tile by tile, but we have not yet found the time to implement this.

Cyril

from chromosight.

Hi Cyril,

Thanks so much for replying so fast. I'll try both suggestions --threads=1 and/or lower resolution.

Regards
Jorge

from chromosight.