All 0 in the output

[DinahBack]

hi, i run ./read_haps --fa hg38.fa bqsr.bam high_quality_markers_deCODE_2015.txt genotyper.vcf.gz , and the value of the output log is 0: SNP_PAIRS ERROR_PAIRS DOUBLE_ERROR_PAIR_COUNT DOUBLE_ERROR_FRACTION REL_ERROR_FRACTION NONSENSE_FRACTION PASS_FAIL REASON
0 0 0 0 0 0 FAIL READ_PAIR_COUNT
Some head log is :parsed args
read pos used file
read VCF header
read pos used file
read VCF header
reading VCF file file chr1
reading VCF file file chr10
reading VCF file file chr11
reading VCF file file chr12
reading VCF file file chr13
reading VCF file file chr14
reading VCF file file chr15
reading VCF file file chr16
reading VCF file file chr17
reading VCF file file chr18
reading VCF file file chr19
reading VCF file file chr2
reading VCF file file chr20
reading VCF file file chr21
reading VCF file file chr22
reading VCF file file chr3
reading VCF file file chr4
reading VCF file file chr5
reading VCF file file chr6
reading VCF file file chr7
reading VCF file file chr8
reading VCF file file chr9
chr1 0
chr10 0
chr11 0
chr12 0
chr13 0
chr14 0
chr15 0
chr16 0
chr17 0
chr18 0
chr19 0
chr2 0
chr20 0
chr21 0
chr22 0
chr3 0
chr4 0
chr5 0
chr6 0
chr7 0
chr8 0
chr9 0
bam file scan chr1
reading Bam region chr1 1 248956422
added DP8480017159TRL1C048R02502139177.

[bjarnivh]

This means that none of your reads match the requirements. Either 1) You have a very small file and no heterozygous overlapping the input marker set or 2) The reads have some flag that so that they are not allowed through the filtering requirements.