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Demultiplexing scRNAseq data using popscle

Hi everyone! I need to run popscle to perform demultiplex of scRNA-seq data. Im just beginning with tutorial data but the dsc-pileup stop with segmentation fault and without any error/informative message. This is the code that I'm using (very similar to tutorial)

./bin/popscle dsc-pileup --sam ../data/jurkat_293t_downsampled_n500_full_bam.bam --vcf ../data/jurkat_293t_exons_only.vcf.withAF.vcf.gz  --out ../data/result

And the terminal output is:

[cramore dsc-pileup] -- Produce pileup of dsc-RNAseq
NOTICE [2024/03/14 15:14:39] - Finished loading 737280 droplet/cell barcodes to consider
NOTICE [2024/03/14 15:14:39] - Initializing BCF reader..
NOTICE [2024/03/14 15:14:39] - Finished identifying 2 samples to load from VCF/BCF
NOTICE [2024/03/14 15:14:39] - Initializing SAM reader..
NOTICE [2024/03/14 15:14:39] - Identified 25 overlapping chromosomes between VCF and BAM
zsh: segmentation fault  ./bin/popscle dsc-pileup --sam  --vcf  --group-list  --out

Does anyone know how I can solve this error? Maybe is important to consider that I'm using macOS

segmentation-fault demultiplex popscle
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written by valentinapazom • valentinapazom

1 answer

I think it was a memory problem because I ran it on another computer with more memory RAM and it worked fine.

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written by valentinapazom • valentinapazom

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