When running Artic on a sample with too few reads, resulting in too small coverage, Longshot automatically calculates the maximum coverage as 0, and fails. We're having issues with that in an automatic pipeline, where some of our samples keep failing due to that, since they have too few reads (as expected, since they were negative samples).
Running: longshot -P 0 -F -A --no_haps --bam barcode91.primertrimmed.rg.sorted.bam --ref primer_schemes/SARS-CoV-2/V1200/SARS-CoV-2.reference.fasta --out barcode91.merged.vcf --potential_variants barcode91.merged.vcf.gz
Command failed:longshot -P 0 -F -A --no_haps --bam barcode91.primertrimmed.rg.sorted.bam --ref primer_schemes/SARS-CoV-2/V1200/SARS-CoV-2.reference.fasta --out barcode91.merged.vcf --potential_variants barcode91.merged.vcf.gz
Command failed:artic-tools check_vcf --summaryOut barcode91.vcfreport.txt --vcfOut barcode91.merged.filtered.vcf barcode91.merged.vcf.gz primer_schemes/SARS-CoV-2/V1200/SARS-CoV-2.scheme.bed 2> barcode91.vcfcheck.log
bcftools view barcode91.merged.vcf.gz
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##medaka_version=1.2.3
##INFO=<ID=DP,Number=1,Type=Integer,Description="Depth of reads at pos">
##INFO=<ID=DPS,Number=2,Type=Integer,Description="Depth of reads at pos by strand (fwd, rev)">
##INFO=<ID=DPSP,Number=1,Type=Integer,Description="Depth of reads spanning pos +-25">
##INFO=<ID=SR,Number=.,Type=Integer,Description="Depth of spanning reads by strand which best align to each allele (ref fwd, ref rev, alt1 fwd, alt1 rev, etc.)">
##INFO=<ID=AR,Number=2,Type=Integer,Description="Depth of ambiguous spanning reads by strand which align equally well to all alleles (fwd, rev)">
##INFO=<ID=SC,Number=.,Type=Integer,Description="Total alignment score to each allele of spanning reads by strand (ref fwd, ref rev, alt1 fwd, alt1 rev, etc.) aligned with parasail match 5, mismatch -4, open 5, extend 3">
##INFO=<ID=Pool,Number=1,Type=String,Description="The pool name">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Medaka genotype.">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Medaka genotype quality score">
##bcftools_viewVersion=1.10.2+htslib-1.10.2
##bcftools_viewCommand=view barcode91.merged.vcf.gz; Date=Mon Aug 23 12:36:40 2021
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
$ artic-tools check_vcf --summaryOut barcode91.vcfreport.txt --vcfOut barcode91.merged.filtered.vcf barcode91.merged.vcf.gz primer_schemes/SARS-CoV-2/V1200/SARS-CoV-2.scheme.bed
[12:35:34] [artic-tools::check_vcf] starting VCF checker
[12:35:34] [artic-tools::check_vcf] reading scheme
[12:35:34] [artic-tools::check_vcf] collecting scheme stats
[12:35:34] [artic-tools::check_vcf] primer scheme file: primer_schemes/SARS-CoV-2/V1200/SARS-CoV-2.scheme.bed
[12:35:34] [artic-tools::check_vcf] reference sequence: MN908947.3
[12:35:34] [artic-tools::check_vcf] number of pools: 2
[12:35:34] [artic-tools::check_vcf] number of primers: 58 (includes 0 alts)
[12:35:34] [artic-tools::check_vcf] minimum primer size: 22
[12:35:34] [artic-tools::check_vcf] maximum primer size: 30
[12:35:34] [artic-tools::check_vcf] number of amplicons: 29
[12:35:34] [artic-tools::check_vcf] mean amplicon size: 1091
[12:35:34] [artic-tools::check_vcf] maximum amplicon size: 1177
[12:35:34] [artic-tools::check_vcf] scheme ref. span: 30-29790
[12:35:34] [artic-tools::check_vcf] scheme overlaps: 6.5591393%
[12:35:34] [artic-tools::check_vcf] setting parameters
[12:35:34] [artic-tools::check_vcf] output report: barcode91.vcfreport.txt
[12:35:34] [artic-tools::check_vcf] filtering variants: true
[12:35:34] [artic-tools::check_vcf] output VCF: barcode91.merged.filtered.vcf
[12:35:34] [artic-tools::check_vcf] minimum quality threshold: 10.0
[12:35:34] [artic-tools::check_vcf] reading VCF file
Segmentation fault (core dumped)