search

statgen / demuxlet

Genetic multiplexing of barcoded single cell RNA-seq
Apache License 2.0
116 stars 25 forks source link

Segmentation fault after initializing SAM reader #107

Open littmanr16 opened 11 months ago

littmanr16 commented 11 months ago

Hello,

I'm trying to use popscle dsc-pileup and am getting a Segmentation fault after Initializing SAM reader:

NOTICE [2023/09/01 14:40:15] - Finished loading 12910 droplet/cell barcodes to consider NOTICE [2023/09/01 14:40:15] - Initializing BCF reader.. NOTICE [2023/09/01 14:40:15] - Finished loading 10 IDs NOTICE [2023/09/01 14:40:15] - Finished identifying 10 samples to load from VCF/BCF NOTICE [2023/09/01 14:40:15] - Initializing SAM reader.. Segmentation fault

I have already removed biallelic and non-autosomal genes from the vcf.

Do you have any ideas how to resolve this?

I have more than enough memory (256Gb) so that shouldn't be a problem

ilyakorsunsky commented 10 months ago

@littmanr16 Any updates on this? I'm experiencing the same issue.

littmanr16 commented 10 months ago

I don't remember exactly but I think it had to do with mismatch in names between the vcf and the reference used to align the scRNAseq data so also in the bam. I believe modifying the vcf to fit the same format as the bam worked. I did a number of things to modify the vcf to get it to work but I don't remember which one solved this specific problem.