iteration limit reached

[Zepeng-Mu]

Hi,

I am creating a singleR object and got the warning message "iteration limit reached". This seems to be an issue with linear model while using regress.out = "nUMI" I guess?

Is it OK if I just ignore this warning message?

Many thanks!

[dviraran]

Hi,

If its connected to the regress.out its something with Seurat, not with SingleR.

If its from SingleR, I wonder where its coming from. Can you copy what is printed out during the run?

Best, Dvir

[Zepeng-Mu]

Sure, this is what I got:

[1] "ST83_integrated"
[1] "Reading single-cell data..."
[1] "Create Seurat object..."
iteration limit reachediteration limit reachediteration limit reachediteration limit reachediteration limit reachediteration limit reachediteration limit reachediteration limit reachediteration limit reachediteration limit reachediteration limit reachediteration limit reachediteration limit reachediteration limit reachediteration limit reachediteration limit reachediteration limit reachediteration limit reachediteration

the iteration limit reached would be repeated for many times, and then:

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

Number of nodes: 4074
Number of edges: 134738

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9212
Number of communities: 20
Elapsed time: 0 seconds
[1] "Creat SingleR object..."
[1] "Dimensions of counts data: 18251x4074"
[1] "Annotating data with HPCA..."
[1] "Variable genes method: de"
[1] "Number of DE genes:3685"
[1] "Number of cells: 4074"
[1] "Fine-tuning round on top cell types (using 16 CPU cores):"
  |=                                                                                   |   1%, ETA 02:35

Thanks

[dviraran]

Yeah, definitely happening while running Seurat code. If the Seurat object is fine I guess you can disregard it.

[Zepeng-Mu]

Yes, indeed. I also found several issues on the Seurat repo. It seems that the warning can be ignored.

Thanks!