WARNING! NOT CONVERGENT!

[stroke1989]

Hi,
Thanks for this tool, when I used copykat to analyze my scRNAseq data, I got warnning as below:
epn_2 = read_rds(file = "epn_2_postfilter.rds")
epn_2.rawdata <- as.matrix(epn_2@assays$RNA@counts)
epn_2.copykat.result <- copykat(rawmat=epn_2.rawdata, id.type="S", ngene.chr=5, win.size=25, KS.cut=0.1, sam.name="epn_2", distance="euclidean", norm.cell.names="",output.seg="FALSE", plot.genes="TRUE", genome="hg20",n.cores=60)
[1] "running copykat v1.1.0"
[1] "step1: read and filter data ..."
[1] "24856 genes, 9037 cells in raw data"
[1] "8924 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= 297
number of iterations= 367
number of iterations= 165
number of iterations= 449
number of iterations= 297
number of iterations= 264
[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"
WARNING! NOT CONVERGENT!
number of iterations= 500
[1] "cell: 4"
number of iterations= 168
[1] "cell: 5"
WARNING! NOT CONVERGENT!
number of iterations= 500
[1] "cell: 6"
WARNING! NOT CONVERGENT!
number of iterations= 500
[1] "cell: 7"
WARNING! NOT CONVERGENT!
number of iterations= 500
[1] "cell: 8"
WARNING! NOT CONVERGENT!
number of iterations= 500
[1] "cell: 9"
WARNING! NOT CONVERGENT!
number of iterations= 500
[1] "cell: 10"
WARNING! NOT CONVERGENT!
number of iterations= 500
[1] "cell: 11"
WARNING! NOT CONVERGENT!
number of iterations= 500

could anyone help me out? Appreciate!

[hyq9588]

I met the same question

[mbihie]

Did you find an answer?

[RijndertAriese]

I encountered the same problem, unfortunately. Does anyone have an idea on what the cause of this warning is and/or what it means for the output?

[zhangsiyao618]

#26, I encountered the same problem, maybe this reply will help ?