Error in analysis of an epithelial cluster

[andrianamanousidaki]

Thank you for the great tool you have provided us!

I am analyzing a cluster of epithelial annotated cells sampled from a tumor, but for some reason the pipelineCNA stops.
Some plots are created and saved but I can not access the data set with classification of the cells.

So my questions are:

1. Do you know why I am seeing the error message attached below?
2. Based on your experience and the output below, is it reasonable that the epithelial cluster has only 56 cells classified as normal cells?

Please find below my code and the error message produced.

Thank you!
Andriana

cpn_fb9 <- pipelineCNA(fibroblasts_9@assays$RNA@counts, sample = "FB9",
                        SUBCLONES = TRUE,
                      plotTree = FALSE,
                      par_cores = 4)

[1] " raw data - genes: 24225 cells: 471"
[1] "1) Filter: cells > 200 genes"
[1] "2) Filter: genes > 10% of cells"
[1] "7650 genes past filtering"
[1] "3) Annotations gene coordinates"
[1] "found 30 confident non malignant cells"
[1] "7225 genes annotated"
[1] "4) Filter: genes involved in the cell cycle"
[1] "6855 genes past filtering "
[1] "5)  Filter: cells > 5genes per chromosome "
[1] "6) Log Freeman Turkey transformation"
[1] "A total of 395 cells, 6855 genes after preprocessing"
[1] "7) Measuring baselines (confident normal cells)"
[1] "8) Smoothing data"
[1] "9) Segmentation (VegaMC)"
[1] "10) Adjust baseline"
1] "11) plot heatmap"
[1] "found 56 tumor cells"
[1] "time classify tumor cells:  1.28261011838913"
Warning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE,  :
  You're computing too large a percentage of total singular values, use a standard svd instead.