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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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Run stalling? #17

Closed dpcook closed 3 years ago

dpcook commented 3 years ago

Hi there--hope all is well!

I have a droplet dataset of ~15k cells from two donors that I'm hoping to demultiplex. I set up a run with the genome1K.phase3.SNP_AF5e2.chr1toX.hg38.vcf.gz. The run initiated with a few lines of output and then hung for 3 days without changing. Any idea what could be going on?

Shellscript: (copied from the docs and forgot to increase -p)

#!/bin/bash
#SBATCH -c 32
#SBATCH --mem=32000 #Maybe should have allocated more memory?
#SBATCH -t 5-10:00:00 

conda activate vireo

BAM="/global/scratch/hpc3837/projects/ardolino/sarcoma/data/ARD6-SC/outs/possorted_genome_bam.bam"
BARCODE="/global/scratch/hpc3837/projects/ardolino/sarcoma/data/ARD6-SC/outs/filtered_feature_bc_matrix/barcodes.tsv.gz"
OUTDIR="/global/scratch/hpc3837/projects/ardolino/sarcoma/output/snp_calls"
REGION_VCF="/global/home/hpc3837/genomes/snp_list/genome1K.phase3.SNP_AF5e2.chr1toX.hg38.vcf.gz"

cellsnp-lite -s $BAM -b $BARCODE -O $OUT_DIR -R $REGION_VCF -p 20 --minMAF 0.1 --minCOUNT 20 --gzip

Output:

[I::main] start time: 2021-05-03 17:16:06
[I::main] mode2: pileup 22 whole chromosomes in 15669 single cells.
[W::csp_pileup_core] Max depth set to maximum value (2147483647)
[I::csp_pileup_core][Thread-0] processing chrom 1 ...
[W::csp_pileup_core] Max depth set to maximum value (2147483647)
[I::csp_pileup_core][Thread-1] processing chrom 2 ...
[W::csp_pileup_core] Max depth set to maximum value (2147483647)
[I::csp_pileup_core][Thread-2] processing chrom 3 ...
[W::csp_pileup_core] Max depth set to maximum value (2147483647)
[I::csp_pileup_core][Thread-3] processing chrom 4 ...
[W::csp_pileup_core] Max depth set to maximum value (2147483647)
[I::csp_pileup_core][Thread-4] processing chrom 5 ...
[W::csp_pileup_core] Max depth set to maximum value (2147483647)
[I::csp_pileup_core][Thread-5] processing chrom 6 ...
[W::csp_pileup_core] Max depth set to maximum value (2147483647)
[I::csp_pileup_core][Thread-6] processing chrom 7 ...
[W::csp_pileup_core] Max depth set to maximum value (2147483647)
[I::csp_pileup_core][Thread-7] processing chrom 8 ...
[W::csp_pileup_core] Max depth set to maximum value (2147483647)
[I::csp_pileup_core][Thread-8] processing chrom 9 ...
[W::csp_pileup_core] Max depth set to maximum value (2147483647)
[I::csp_pileup_core][Thread-9] processing chrom 10 ...
[W::csp_pileup_core] Max depth set to maximum value (2147483647)
[I::csp_pileup_core][Thread-10] processing chrom 11 ...
[W::csp_pileup_core] Max depth set to maximum value (2147483647)
[I::csp_pileup_core][Thread-11] processing chrom 12 ...
[W::csp_pileup_core] Max depth set to maximum value (2147483647)
[I::csp_pileup_core][Thread-12] processing chrom 13 ...
[W::csp_pileup_core] Max depth set to maximum value (2147483647)
[I::csp_pileup_core][Thread-13] processing chrom 14 ...
[W::csp_pileup_core] Max depth set to maximum value (2147483647)
[I::csp_pileup_core][Thread-14] processing chrom 15 ...
[W::csp_pileup_core] Max depth set to maximum value (2147483647)
[I::csp_pileup_core][Thread-15] processing chrom 16 ...
[W::csp_pileup_core] Max depth set to maximum value (2147483647)
[I::csp_pileup_core][Thread-16] processing chrom 17 ...
[W::csp_pileup_core] Max depth set to maximum value (2147483647)
[I::csp_pileup_core][Thread-17] processing chrom 18 ...
[W::csp_pileup_core] Max depth set to maximum value (2147483647)
[I::csp_pileup_core][Thread-18] processing chrom 19 ...
[W::csp_pileup_core] Max depth set to maximum value (2147483647)
[I::csp_pileup_core][Thread-19] processing chrom 20 ...
slurmstepd: error: *** JOB 4776148 ON cac026 CANCELLED AT 2021-05-06T09:38:26 ***

I appreciate it!

David

hxj5 commented 3 years ago

Hi David,

Thanks for your feedback. The output log seems strange with [I::main] mode2: pileup 22 whole chromosomes in 15669 single cells. As the -R $REGION_VCF option was specified in the script, cellsnp-lite should be in mode 1 (genotyping with given SNPs) instead of mode 2 (de novo genotyping without given SNPs).

Was the latest version (v1.2.0) of cellsnp-lite you were using? you could check with cellsnp-lite -V.

Xianjie

dpcook commented 3 years ago

Hi Xianjie--thanks for the quick reply. I confirmed that it was v1.2.0, but also noticed the silly error I made.

I defined $OUTDIR but then called $OUT_DIR right before setting -R. Must prevent it from reading through the other parameters or something.

Fixed the call and it seems to start mode 1 properly:

cellsnp-lite -s $BAM -b $BARCODE -O $OUTDIR -R $REGION_VCF -p 20 --minMAF 0.1 --minCOUNT 20 --gzip
[I::main] start time: 2021-05-13 10:59:05
[I::main] loading the VCF file for given SNPs ...
[I::main] fetching 7352497 candidate variants ...
[I::main] mode 1: fetch given SNPs in 15669 single cells.