[E::csp_pileup] could not parse name for chrom 20

[PietroD]

Hi, thanks for the tools. I am getting this error when trying mode 2a.

My command:

cellsnp-lite -s possorted_genome_bam.bam -b filtered_feature_bc_matrix/barcodes.tsv.gz -O cellsnp_out/ -p 22 --minMAF 0.1 --minCOUNT 100 --gzip

Output:

[I::main] start time: 2021-11-30 17:41:00 [W::check_args] Max depth set to maximum value (2147483647) [I::main] mode 2a: pileup 22 whole chromosomes in 5219 single cells. [E::csp_pileup] could not parse name for chrom 20. [E::main] running mode 2a failed. [E::main] Quiting... [I::main] end time: 2021-11-30 17:41:00 [I::main] time spent: 0 seconds.

I am working with cellsnp-lite 1.2.2 (htslib 1.12)

Thanks

[hxj5]

Hi, thanks for your feedback. Is this a dataset for mouse? If yes, please refer to issue 3.