sc_demultiplex empty output

[cpattaroni]

Hi,

sc_demultiplex_and_count is running till the end without bugging but then the count folder is empty (no .csv written). It is quite frustrating, as there is no error so no idea why it is not working.

> sc_demultiplex_and_count(inbam = 'alignment/map_01.bam',
+                outdir = 'demultiplexed_01',
+                has_UMI = TRUE,
+                bc_anno = 'Samples_barcodes.csv',
+                UMI_cor = 1,
+                gene_fl = FALSE,
+                nthreads = nc)
demultiplexing reads by barcode...
time elapsed: 29 minutes 6 seconds

summarising gene counts...
time elapsed: 2 milliseconds

[MiladAD123NGS]

Hi

I have this problem, too.
Multi threading also doesn't work.
I'm analyzing a drop-seq data and now I wanna put scPipe into the trash!

>   sc_demultiplex(file.path(data_dir, "out.map.bam"), "/media/ad-bioinformatics/9117284696_AD/dd/main/zzzzzz",
                  barcode_annotation_fn, mito = "chrMT", has_UMI = TRUE, max_mis = 2,
                  nthreads = 8)


demultiplexing reads by barcode...
time elapsed: 127 minutes 41 seconds