FindClusters is taking too long for ~700K cells

[buutrg]

Hi Seurat developers, I am using add Cluster on a 700K cells dataset, and it froze after Running Louvain algorithm for 12 hours. I have tried using default parameters with resolution = 1.5 and 1.8

Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 694117
Number of edges: 8990440

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9372
Number of communities: 11279
Elapsed time: 249 seconds

Is this a normal behavior? Do you know how to solve this?

Thank you!

[sunhang526]

I have the similar problem now, have you solved it? please

[lizchcase]

Not sure if you already found your way through this but 700k is a ton of cells! This is great experimentally but will require a lot of computational resources. The amount of time it would take depends a lot on the specs of the computer/cluster you're running on. Generally, running with more nodes will make this go faster, and you will likely require quite a bit of memory/RAM

[xinglei01]

"Hello developers, I have a question. When the number of cells reaches over a million, the running speed of FindClusters with default parameters is too slow. Can I set singleton=F? What is the essential purpose of this parameter?"