Strange warnings occurred during the procedure about too-many-cells HOT 3 CLOSED

The issue is that you are forcing the cells to have new barcodes with -Z (so AAACCTGAGAGACTAT-1 would become AAACCTGAGAGACTAT-1-6N-total and have the label of 6N-total) but you have the (I assume) old barcodes in your labels file. So essentially, -Z was created to avoid having to make a labels file if each matrix was basically a sample and to avoid cases with overlapping barcodes (by appending the sample name to the barcode). So in this case, you can either not use the labels file or not use -Z (and preferably update your barcodes so they don't overlap, like -2 instead of -1 for instance).

from too-many-cells.

Thank you very much! I got the result successfully.

BTW, I would like to know that if I want to focus on a subset of the cells in the tree, I should select the cells by myself at first, then run too-many-cells, right?

from too-many-cells.

You can use --root-cut to create a new root in the tree, hopefully that is what you are looking for.

from too-many-cells.