Running a million cells failed in the docker
minghlijiyi opened this issue · 2 comments
Hi Gregory, I installed the package in the docker. I gave 15g RAM to the docker, it is the maximum RAM. It runs well for 500,000 cells, However, it runs failed for a million cells. Could you give me some help? I used the below codes. Thank you.
docker run -it --rm -v "/home/username:/home/username"
-m 15g
gregoryschwartz/too-many-cells:2.0.0.0 make-tree
--matrix-path /home/username/path/to/input
--labels-file /home/username/path/to/labels.csv
--draw-collection "PieRing"
--output /home/username/path/to/out
> clusters.csv
too-many-cells will try to use all features for the most accurate result. However, with many cells this will take even more time and space. I recommend using dimensionality reduction to reduce the feature space upstream of too-many-cells, or try using the built in one (--lsa) to see if it can handle it first.
It works, thank you so much!