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statgen / demuxlet

Genetic multiplexing of barcoded single cell RNA-seq
Apache License 2.0
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WARNING: Cannot find AF field from INFO field in VCF file, now calculate AF from AC/AN. Segmentation fault #92

Open changostraw opened 2 years ago

changostraw commented 2 years ago

I am new to demuxlet and running demuxlet as part of demuxafy within a container:

singularity exec --bind /project/rrg-gturecki/Sarah/multiplex_test_demuxify_run2_cecum_poolC/outs/raw_feature_bc_matrix Demuxafy.sif popscle dsc-pileup --sam multiplex_test_demuxify_run2_cecum_poolC/outs/possorted_genome_bam.bam --vcf header_sorted_corrected_combined_multiplex_test_genotypes.vcf --group-list multiplex_test_demuxify_run2_cecum_poolC/outs/raw_feature_bc_matrix/barcodes.tsv.gz --out /project/rrg-gturecki/Sarah/multiplex_test_demuxify_run2_cecum_poolC/demuxlet_pileup

I get this response: [cramore dsc-pileup] -- Produce pileup of dsc-RNAseq

Copyright (c) 2009-2017 by Hyun Min Kang and Adrian Tan Licensed under the Apache License v2.0 http://www.apache.org/licenses/

Available Options

The following parameters are available. Ones with "[]" are in effect: Options for input SAM/BAM/CRAM : --sam [multiplex_test_demuxify_run2_cecum_poolC/outs/possorted_genome_bam.bam], --tag-group [CB], --tag-UMI [UB], --exclude-flag [1796] Options for input VCF/BCF : --vcf [header_sorted_corrected_combined_multiplex_test_genotypes.vcf], --sm, --sm-list Output Options : --out [/project/rrg-gturecki/Sarah/multiplex_test_demuxify_run2_cecum_poolC/demuxlet_pileup], --sam-verbose [1000000], --vcf-verbose [10000], --skip-umi SNP-overlapping Read filtering Options : --cap-BQ [40], --min-BQ [13], --min-MQ [20], --min-TD, --excl-flag [3844] Cell/droplet filtering options : --group-list [multiplex_test_demuxify_run2_cecum_poolC/outs/raw_feature_bc_matrix/barcodes.tsv.gz], --min-total, --min-uniq, --min-snp

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

NOTICE [2022/05/30 09:33:04] - Finished loading 1051074 droplet/cell barcodes to consider NOTICE [2022/05/30 09:33:04] - Initializing BCF reader.. NOTICE [2022/05/30 09:33:04] - Finished identifying 5 samples to load from VCF/BCF NOTICE [2022/05/30 09:33:04] - Initializing SAM reader.. NOTICE [2022/05/30 09:33:04] - Identified 25 overlapping chromosomes between VCF and BAM NOTICE [2022/05/30 09:33:04] - WARNING: Cannot find AF field from INFO field in VCF file, now calculate AF from AC/AN Segmentation fault

There is no FATAL ERROR or specific problem identified or further explanation of what went wrong. Does anyone have any ideas of what the issue is? thanks!

changostraw commented 2 years ago

I tried increasing memory allocation to 250G, but it doesn't help. Usually if there is a memory issue the cluster will say it was killed because it exceeded the memory allocated, so I think this is more likely to be a bug.

changostraw commented 2 years ago

Hi, I am still getting a general segmentation fault with no specific error. I have checked the vcf file and bam file and everything is in format agreement. I have increased memory. Has anyone else had this issue? I am not sure where to start as there is no specifics on where it is crashing. Thanks!