Running MultiK on one single cell sample, is it that memory intensive
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6 months ago
mropri ▴ 150

Hi,

I was running MultiK on my seurat object that has cells from one sample. I have submitted this as a job using a range of memories (128Gb - 240Gb). However, for each I keep getting this error:

/var/spool/slurmd/job29495997/slurm_script: line 18:  7475 Killed                  Rscript /home/alr2523/scripts/Rscripts/MultiK.R
slurmstepd: error: Detected 1 oom_kill event in StepId=29495997.batch. Some of the step tasks have been OOM Killed.

I know this indicates that the memory provided for some tasks was not enough. My question is that is MultiK that memory intensive that even at 240Gb of memory provided, it is not enough? Also, what can be another strategy to run MultiK on my seurat object? Would it be best to subset to 70% cells to run MultiK as that would hopefully require less memory than I can give it at max (250Gb)? Appreciate any help.

MultiK Single-Cell • 224 views
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