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single-cell-genetics / cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells
https://cellsnp-lite.readthedocs.io
Apache License 2.0
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running mode 2 failed #3

Closed mengchengyao closed 3 years ago

mengchengyao commented 3 years ago

Thank you for your great tools with cellsnp-lite. I got an error with running mode 2 failed, and i do not known and no usefull information.

[E::pileup_regions] could not parse name for chrom 21. [I::pileup_regions][Thread-18] has pileup-ed in total 212 SNPs for chrom 19 [I::pileup_regions][Thread-17] has pileup-ed in total 220 SNPs for chrom 18 [I::pileup_regions][Thread-15] has pileup-ed in total 131 SNPs for chrom 16 [I::pileup_regions][Thread-14] has pileup-ed in total 216 SNPs for chrom 15 [I::pileup_regions][Thread-12] has pileup-ed in total 223 SNPs for chrom 13 [I::pileup_regions][Thread-13] has pileup-ed in total 235 SNPs for chrom 14 [I::pileup_regions][Thread-7] has pileup-ed in total 377 SNPs for chrom 8 [I::pileup_regions][Thread-16] has pileup-ed in total 388 SNPs for chrom 17 [I::pileup_regions][Thread-11] has pileup-ed in total 251 SNPs for chrom 12 [I::pileup_regions][Thread-9] has pileup-ed in total 252 SNPs for chrom 10 [I::pileup_regions][Thread-8] has pileup-ed in total 271 SNPs for chrom 9 [I::pileup_regions][Thread-3] has pileup-ed in total 366 SNPs for chrom 4 [I::pileup_regions][Thread-5] has pileup-ed in total 317 SNPs for chrom 6 [I::pileup_regions][Thread-2] has pileup-ed in total 305 SNPs for chrom 3 [I::pileup_regions][Thread-10] has pileup-ed in total 669 SNPs for chrom 11 [I::pileup_regions][Thread-1] has pileup-ed in total 480 SNPs for chrom 2 [I::pileup_regions][Thread-0] has pileup-ed in total 461 SNPs for chrom 1 [I::pileup_regions][Thread-6] has pileup-ed in total 535 SNPs for chrom 7 [I::pileup_regions][Thread-4] has pileup-ed in total 381 SNPs for chrom 5 [E::main] running mode 2 failed. [E::main] Quiting... [I::main] end time: 2020-11-04 20:44:23 [I::main] time spent: 81957 seconds.

Yours

mengchengyao commented 3 years ago

And my cmd as follows cellsnp-lite -s 10x_possorted_genome_bam.bam -b barcodes.tsv -O outdir -p 22 --minMAF 0.1 --minCOUNT 100 --gzip

The bam was from cellranger with single cell RNA case.

huangyh09 commented 3 years ago

For mode2, by default it runs on chr1 to 22 on human. For mouse, you need to specify it to 1,2,...,19 (replace the ellipsis).

On the other hand, if it is lab straint with genotype available, e.g., from the mouse genome project (ftp://ftp-mouse.sanger.ac.uk/current_snps), you can also run mode 1.

Yuanhua