[init] ff = 0.050
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG00136_x_HG00290_FF_5.mix.bam
[W::hts_idx_load3] The index file is older than the data file: HG00136_x_HG00290_FF_5.mix.bam.bai
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 628 sites
[chrom] starting chr1
[chrom] chr1 done in 13.8s
[chrom] starting chr2
[chrom] chr2 done in 6.7s
[chrom] starting chr3
[progress] 100 variants processed (ok=100 no_reads=0 ref_mismatch=0 other=0) elapsed=22.9s rate=4.4/s
[chrom] chr3 done in 11.9s
[chrom] starting chr4
[chrom] chr4 done in 12.1s
[chrom] starting chr5
[chrom] chr5 done in 5.7s
[chrom] starting chr6
[progress] 200 variants processed (ok=200 no_reads=0 ref_mismatch=0 other=0) elapsed=57.8s rate=3.5/s
[chrom] chr6 done in 11.1s
[chrom] starting chr7
[chrom] chr7 done in 8.9s
[chrom] starting chr8
[chrom] chr8 done in 3.6s
[chrom] starting chr9
[progress] 300 variants processed (ok=300 no_reads=0 ref_mismatch=0 other=0) elapsed=81.1s rate=3.7/s
[chrom] chr9 done in 7.4s
[chrom] starting chr10
[chrom] chr10 done in 3.6s
[chrom] starting chr11
[chrom] chr11 done in 15.8s
[chrom] starting chr12
[chrom] chr12 done in 9.4s
[chrom] starting chr13
[progress] 400 variants processed (ok=400 no_reads=0 ref_mismatch=0 other=0) elapsed=110.6s rate=3.6/s
[chrom] chr13 done in 2.7s
[chrom] starting chr14
[chrom] chr14 done in 5.6s
[chrom] starting chr15
[chrom] chr15 done in 7.4s
[chrom] starting chr16
[chrom] chr16 done in 6.6s
[chrom] starting chr17
[progress] 500 variants processed (ok=500 no_reads=0 ref_mismatch=0 other=0) elapsed=138.7s rate=3.6/s
[chrom] chr17 done in 12.0s
[chrom] starting chr18
[chrom] chr18 done in 2.1s
[chrom] starting chr19
[chrom] chr19 done in 12.6s
[chrom] starting chr20
[progress] 600 variants processed (ok=600 no_reads=0 ref_mismatch=0 other=0) elapsed=161.5s rate=3.7/s
[chrom] chr20 done in 5.2s
[chrom] starting chr21
[chrom] chr21 done in 2.3s
[chrom] starting chr22
[chrom] chr22 done in 3.7s
[done] 630 variants in 170.1s (ok=630 no_reads=0 ref_mismatch=0 other=0)