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LuyiTian / scPipe

a pipeline for single cell RNA-seq data analysis
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sc_demultiplex empty output #131

Open cpattaroni opened 3 years ago

cpattaroni commented 3 years ago

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 commented 2 years ago

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