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statgen / demuxlet

Genetic multiplexing of barcoded single cell RNA-seq
Apache License 2.0
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Segmentation fault #39

Closed ONeillMB1 closed 5 years ago

ONeillMB1 commented 5 years ago

Thanks for developing this tool. I am trying to get the program working on a subset of my data before running it on the complete dataset. I have extracted some 10X genomics reads mapping to chromosome 22 (test.bam) and run the following command:

demuxlet --sam test.sam --tag-group CB --tag-UMI UB --vcf pilot2.vcf --field GT --geno-error 0.01 --out test_run

Which throws the following error.

Available Options

The following parameters are available. Ones with "[]" are in effect: Options for input SAM/BAM/CRAM : --sam [test.sam], --tag-group [CB], --tag-UMI [UB] Options for input VCF/BCF : --vcf [pilot2.vcf], --field [GT], --geno-error [0.01], --min-mac [1], --min-callrate [0.50], --sm, --sm-list Output Options : --out [test_run], --alpha, --write-pair, --doublet-prior [0.50], --sam-verbose [1000000], --vcf-verbose [10000] Read filtering Options : --cap-BQ [40], --min-BQ [13], --min-MQ [20], --min-TD, --excl-flag [3844] Cell/droplet filtering options : --group-list, --min-total, --min-uniq, --min-snp

Run with --help for more detailed help messages of each argument.

NOTICE [2019/03/11 14:31:53] - Finished identifying 8 samples to load from VCF/BCF

FATAL ERROR - Segmentation fault

Samtools has no problem with the bam/sam files so I'm not sure why I am getting a segmentation fault. Any ideas what is going on?

ONeillMB1 commented 5 years ago

It is because my chromosomes are named differently in the VCF vs the BAM. Sorry - closing.