WARNING! NOT CONVERGENT! number of iterations= 500

No repository file or test is identified. Reproduce the report using the supplied R code, Seurat object, and copykat parameters, then inspect the step 4 baseline-measurement path where the non-convergence appears. Done means identifying a reproducible cause and adding a documented or tested correction, if the repository supports one.

I wanted to use copykat to visualize the copy number variation of epithelial cell samples from this paper (R code and downstream analysis objects for the scRNA-seq atlas of normal and tumorigenic human breast tissue). I extracted a raw counts matrix from this seurat object (SeuratObject_TNBCSub.rds) and then filtered for the epithelial cells only. I then ran the copykat.test function on it afterwards and got the error message below. Would anyone happen to know what went wrong? I have also attached my code below. Any help would be appreciated!

code

## **libraries**
#install.packages("devtools")
library(devtools)
#install_github("navinlabcode/copykat")
library(copykat)
#install.packages("Seurat")
library(Seurat)
#install.packages("tidyverse")
library(tidyverse)

## **read seurat object**
tnbc    <- readRDS("~/BRCA/BRCA-data/SeuratObject_TNBCSub.rds")
#updating the object if it won't open
tnbc = UpdateSeuratObject(object = tnbc) #use this if you get Error in eval(call("@", object, slot)) : no slot of name "images" for this object of class "Seurat"
#rename object
tnbc.epi <- tnbc

#rename clusters
tnbc.epi <- RenameIdents(tnbc.epi,
                     '0' = "epithelial",
                     '2' = "epithelial-cycling")

#subset object to just epithelial cells
tnbc.epi <- subset(x = tnbc.epi, idents = c("epithelial", "epithelial-cycling"))

#subset the data to a specific sample
tnbc.epi.4031 <- subset(tnbc.epi, subset = group == "TN_B1_4031")
saveRDS(object = tnbc.epi.4031, "~/BRCA/BRCA-data/tnbc.epi.4031.rds")

## **step 3: run copykat**
#may take a few minutes
copykat.test <- copykat(rawmat=as.matrix(tnbc.epi.4031@assays$RNA@counts), 
                        id.type="S", 
                        ngene.chr=3, 
                        win.size=25, 
                        KS.cut=0.1, 
                        sam.name="test", 
                        distance="euclidean",
                        norm.cell.names="",
                        output.seg="FLASE", 
                        plot.genes="TRUE", 
                        genome="hg20",
                        #LOW.DR = 0.01,
                        #UP.DR = 0.2,
                        n.cores=1)

error message

[1] "running copykat v1.1.0"
[1] "step1: read and filter data ..."
[1] "15403 genes, 5513 cells in raw data"
[1] "8554 genes past LOW.DR filtering"
[1] "step 2: annotations gene coordinates ..."
[1] "start annotation ..."
[1] "step 3: smoothing data with dlm ..."
[1] "step 4: measuring baselines ..."
number of iterations= 223 
number of iterations= 707 
number of iterations= 195 
number of iterations= 590 
number of iterations= 317 
number of iterations= 117 
[1] "low confidence in classification"
[1] "cell: 1"
WARNING! NOT CONVERGENT! 
number of iterations= 500 
[1] "cell: 2"
WARNING! NOT CONVERGENT! 
number of iterations= 500 
[1] "cell: 3"
number of iterations= 256 
[1] "cell: 4"
WARNING! NOT CONVERGENT! 
number of iterations= 500