Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/f9e98f74a941fcba3f1b2047a9c830/.command.sh
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/targets/HG02922_x_HG03063_FF_10.targets.tsv
  Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/vcfs/HG02922_x_HG03063_FF_10.vcf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/9282e2d9c028a1b3d405b20bad43a6/HG02922_x_HG03063_FF_10.mix.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/f9e98f74a941fcba3f1b2047a9c830/.command.run
==> STAGING COMPLETE (7 inputs)

[init] ff = 0.100
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG02922_x_HG03063_FF_10.mix.bam
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 18682 sites
[chrom] starting chr1
[progress] 100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=100) elapsed=0.0s rate=25277.6/s
[progress] 200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=200) elapsed=0.0s rate=23554.2/s
[progress] 300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=300) elapsed=0.0s rate=28808.4/s
[progress] 400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=400) elapsed=0.0s rate=32606.2/s
[progress] 500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=500) elapsed=0.0s rate=33212.2/s
[progress] 600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=600) elapsed=0.0s rate=35861.0/s
[progress] 700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=700) elapsed=0.0s rate=37589.1/s
[progress] 800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=800) elapsed=0.0s rate=38749.1/s
[progress] 900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=900) elapsed=0.0s rate=38801.8/s
[progress] 1000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1000) elapsed=0.0s rate=40553.3/s
[progress] 1100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1100) elapsed=0.0s rate=41791.1/s
[progress] 1200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1200) elapsed=0.0s rate=42948.0/s
[progress] 1300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1300) elapsed=0.0s rate=44042.2/s
[progress] 1400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1400) elapsed=0.0s rate=42943.0/s
[progress] 1500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1500) elapsed=0.0s rate=43359.4/s
[progress] 1600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1600) elapsed=0.0s rate=43629.3/s
[progress] 1700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1700) elapsed=0.0s rate=42929.1/s
[chrom] chr1 done in 0.0s
[chrom] starting chr2
[progress] 1800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1800) elapsed=0.0s rate=43443.3/s
[progress] 1900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1900) elapsed=0.0s rate=43858.5/s
[progress] 2000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2000) elapsed=0.0s rate=43286.9/s
[progress] 2100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2100) elapsed=0.0s rate=43739.5/s
[progress] 2200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2200) elapsed=0.0s rate=44015.2/s
[progress] 2300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2300) elapsed=0.1s rate=44376.2/s
[progress] 2400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2400) elapsed=0.1s rate=44231.9/s
[progress] 2500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2500) elapsed=0.1s rate=44486.0/s
[progress] 2600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2600) elapsed=0.1s rate=44836.2/s
[chrom] chr2 done in 0.0s
[chrom] starting chr3
[progress] 2700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2700) elapsed=0.1s rate=44672.2/s
[progress] 2800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2800) elapsed=0.1s rate=43043.3/s
[progress] 2900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2900) elapsed=0.1s rate=42810.6/s
[progress] 3000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3000) elapsed=0.1s rate=43031.9/s
[progress] 3100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3100) elapsed=0.1s rate=43021.9/s
[progress] 3200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3200) elapsed=0.1s rate=42676.3/s
[progress] 3300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3300) elapsed=0.1s rate=42846.3/s
[progress] 3400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3400) elapsed=0.1s rate=42964.3/s
[progress] 3500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3500) elapsed=0.1s rate=42014.5/s
[chrom] chr3 done in 0.0s
[chrom] starting chr4
[progress] 3600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3600) elapsed=0.1s rate=41913.7/s
[progress] 3700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3700) elapsed=0.1s rate=41921.5/s
[progress] 3800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3800) elapsed=0.1s rate=42037.4/s
[progress] 3900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3900) elapsed=0.1s rate=42247.8/s
[progress] 4000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4000) elapsed=0.1s rate=42095.6/s
[progress] 4100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4100) elapsed=0.1s rate=42288.9/s
[chrom] chr4 done in 0.0s
[chrom] starting chr5
[progress] 4200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4200) elapsed=0.1s rate=42473.9/s
[progress] 4300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4300) elapsed=0.1s rate=42167.6/s
[progress] 4400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4400) elapsed=0.1s rate=42015.6/s
[progress] 4500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4500) elapsed=0.1s rate=42039.1/s
[progress] 4600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4600) elapsed=0.1s rate=42277.1/s
[progress] 4700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4700) elapsed=0.1s rate=42144.9/s
[chrom] chr5 done in 0.0s
[chrom] starting chr6
[progress] 4800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4800) elapsed=0.1s rate=42346.7/s
[progress] 4900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4900) elapsed=0.1s rate=42565.6/s
[progress] 5000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5000) elapsed=0.1s rate=42835.9/s
[progress] 5100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5100) elapsed=0.1s rate=42858.4/s
[progress] 5200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5200) elapsed=0.1s rate=43059.6/s
[progress] 5300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5300) elapsed=0.1s rate=43270.0/s
[progress] 5400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5400) elapsed=0.1s rate=43198.2/s
[progress] 5500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5500) elapsed=0.1s rate=42746.0/s
[progress] 5600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5600) elapsed=0.1s rate=42936.9/s
[progress] 5700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5700) elapsed=0.1s rate=43070.8/s
[chrom] chr6 done in 0.0s
[chrom] starting chr7
[progress] 5800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5800) elapsed=0.1s rate=43239.3/s
[progress] 5900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5900) elapsed=0.1s rate=43129.0/s
[progress] 6000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6000) elapsed=0.1s rate=43229.8/s
[progress] 6100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6100) elapsed=0.1s rate=43460.1/s
[progress] 6200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6200) elapsed=0.1s rate=43392.5/s
[progress] 6300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6300) elapsed=0.1s rate=43122.6/s
[progress] 6400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6400) elapsed=0.1s rate=43101.9/s
[progress] 6500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6500) elapsed=0.2s rate=43315.8/s
[progress] 6600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6600) elapsed=0.2s rate=43559.5/s
[progress] 6700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6700) elapsed=0.2s rate=43437.1/s
[progress] 6800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6800) elapsed=0.2s rate=43530.6/s
[progress] 6900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6900) elapsed=0.2s rate=43717.5/s
[chrom] chr7 done in 0.0s
[chrom] starting chr8
[progress] 7000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7000) elapsed=0.2s rate=43883.2/s
[progress] 7100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7100) elapsed=0.2s rate=43462.4/s
[progress] 7200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7200) elapsed=0.2s rate=43455.4/s
[progress] 7300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7300) elapsed=0.2s rate=43523.6/s
[progress] 7400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7400) elapsed=0.2s rate=43731.0/s
[chrom] chr8 done in 0.0s
[chrom] starting chr9
[progress] 7500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7500) elapsed=0.2s rate=43715.4/s
[progress] 7600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7600) elapsed=0.2s rate=43847.5/s
[progress] 7700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7700) elapsed=0.2s rate=43941.1/s
[progress] 7800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7800) elapsed=0.2s rate=44107.9/s
[progress] 7900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7900) elapsed=0.2s rate=43969.6/s
[progress] 8000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8000) elapsed=0.2s rate=43935.1/s
[progress] 8100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8100) elapsed=0.2s rate=43959.4/s
[chrom] chr9 done in 0.0s
[chrom] starting chr10
[progress] 8200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8200) elapsed=0.2s rate=43994.5/s
[progress] 8300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8300) elapsed=0.2s rate=43880.8/s
[progress] 8400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8400) elapsed=0.2s rate=43987.6/s
[progress] 8500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8500) elapsed=0.2s rate=44099.8/s
[progress] 8600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8600) elapsed=0.2s rate=44259.0/s
[chrom] chr10 done in 0.0s
[chrom] starting chr11
[progress] 8700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8700) elapsed=0.2s rate=44087.8/s
[progress] 8800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8800) elapsed=0.2s rate=44084.9/s
[progress] 8900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8900) elapsed=0.2s rate=44140.5/s
[progress] 9000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9000) elapsed=0.2s rate=44207.2/s
[progress] 9100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9100) elapsed=0.2s rate=44077.9/s
[progress] 9200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9200) elapsed=0.2s rate=44164.1/s
[progress] 9300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9300) elapsed=0.2s rate=44204.4/s
[progress] 9400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9400) elapsed=0.2s rate=44374.9/s
[progress] 9500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9500) elapsed=0.2s rate=44198.7/s
[progress] 9600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9600) elapsed=0.2s rate=44178.4/s
[progress] 9700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9700) elapsed=0.2s rate=44188.7/s
[progress] 9800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9800) elapsed=0.2s rate=44265.5/s
[chrom] chr11 done in 0.0s
[chrom] starting chr12
[progress] 9900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9900) elapsed=0.2s rate=44086.5/s
[progress] 10000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10000) elapsed=0.2s rate=44089.5/s
[progress] 10100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10100) elapsed=0.2s rate=44245.1/s
[progress] 10200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10200) elapsed=0.2s rate=44362.0/s
[progress] 10300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10300) elapsed=0.2s rate=44196.5/s
[progress] 10400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10400) elapsed=0.2s rate=44253.9/s
[progress] 10500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10500) elapsed=0.2s rate=44237.9/s
[progress] 10600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10600) elapsed=0.2s rate=44326.5/s
[progress] 10700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10700) elapsed=0.2s rate=44214.8/s
[chrom] chr12 done in 0.0s
[chrom] starting chr13
[progress] 10800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10800) elapsed=0.2s rate=44267.6/s
[progress] 10900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10900) elapsed=0.2s rate=44358.8/s
[progress] 11000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11000) elapsed=0.2s rate=44464.0/s
[chrom] chr13 done in 0.0s
[chrom] starting chr14
[progress] 11100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11100) elapsed=0.3s rate=44292.7/s
[progress] 11200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11200) elapsed=0.3s rate=44216.9/s
[progress] 11300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11300) elapsed=0.3s rate=44280.5/s
[progress] 11400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11400) elapsed=0.3s rate=44364.8/s
[progress] 11500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11500) elapsed=0.3s rate=44485.4/s
[progress] 11600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11600) elapsed=0.3s rate=44456.1/s
[chrom] chr14 done in 0.0s
[chrom] starting chr15
[progress] 11700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11700) elapsed=0.3s rate=44538.3/s
[progress] 11800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11800) elapsed=0.3s rate=44584.0/s
[progress] 11900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11900) elapsed=0.3s rate=44605.5/s
[progress] 12000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12000) elapsed=0.3s rate=44323.2/s
[chrom] chr15 done in 0.0s
[chrom] starting chr16
[progress] 12100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12100) elapsed=0.3s rate=44282.2/s
[progress] 12200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12200) elapsed=0.3s rate=44327.9/s
[progress] 12300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12300) elapsed=0.3s rate=44251.9/s
[progress] 12400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12400) elapsed=0.3s rate=44392.5/s
[progress] 12500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12500) elapsed=0.3s rate=44519.5/s
[progress] 12600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12600) elapsed=0.3s rate=44612.3/s
[progress] 12700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12700) elapsed=0.3s rate=44704.1/s
[progress] 12800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12800) elapsed=0.3s rate=44598.6/s
[chrom] chr16 done in 0.0s
[chrom] starting chr17
[progress] 12900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12900) elapsed=0.3s rate=44540.4/s
[progress] 13000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13000) elapsed=0.3s rate=44593.2/s
[progress] 13100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13100) elapsed=0.3s rate=44667.0/s
[progress] 13200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13200) elapsed=0.3s rate=44559.3/s
[progress] 13300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13300) elapsed=0.3s rate=44629.3/s
[progress] 13400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13400) elapsed=0.3s rate=44709.2/s
[progress] 13500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13500) elapsed=0.3s rate=44763.4/s
[progress] 13600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13600) elapsed=0.3s rate=44837.5/s
[progress] 13700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13700) elapsed=0.3s rate=44743.3/s
[progress] 13800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13800) elapsed=0.3s rate=44819.5/s
[progress] 13900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13900) elapsed=0.3s rate=44862.2/s
[chrom] chr17 done in 0.0s
[chrom] starting chr18
[progress] 14000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14000) elapsed=0.3s rate=44918.2/s
[progress] 14100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14100) elapsed=0.3s rate=44862.9/s
[chrom] chr18 done in 0.0s
[chrom] starting chr19
[progress] 14200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14200) elapsed=0.3s rate=44904.8/s
[progress] 14300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14300) elapsed=0.3s rate=44960.5/s
[progress] 14400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14400) elapsed=0.3s rate=44873.0/s
[progress] 14500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14500) elapsed=0.3s rate=44934.9/s
[progress] 14600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14600) elapsed=0.3s rate=45048.8/s
[progress] 14700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14700) elapsed=0.3s rate=45143.4/s
[progress] 14800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14800) elapsed=0.3s rate=45184.3/s
[progress] 14900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14900) elapsed=0.3s rate=45280.1/s
[progress] 15000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15000) elapsed=0.3s rate=45227.4/s
[progress] 15100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15100) elapsed=0.3s rate=45308.9/s
[progress] 15200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15200) elapsed=0.3s rate=45394.4/s
[progress] 15300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15300) elapsed=0.3s rate=45483.5/s
[progress] 15400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15400) elapsed=0.3s rate=45554.8/s
[progress] 15500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15500) elapsed=0.3s rate=45517.7/s
[progress] 15600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15600) elapsed=0.3s rate=45567.6/s
[progress] 15700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15700) elapsed=0.3s rate=45635.2/s
[progress] 15800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15800) elapsed=0.3s rate=45686.4/s
[progress] 15900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15900) elapsed=0.3s rate=45701.5/s
[progress] 16000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16000) elapsed=0.4s rate=45679.1/s
[progress] 16100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16100) elapsed=0.4s rate=45783.8/s
[progress] 16200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16200) elapsed=0.4s rate=45869.9/s
[progress] 16300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16300) elapsed=0.4s rate=45908.2/s
[progress] 16400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16400) elapsed=0.4s rate=45995.5/s
[progress] 16500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16500) elapsed=0.4s rate=46087.5/s
[progress] 16600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16600) elapsed=0.4s rate=46037.0/s
[progress] 16700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16700) elapsed=0.4s rate=46135.9/s
[chrom] chr19 done in 0.0s
[chrom] starting chr20
[progress] 16800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16800) elapsed=0.4s rate=46179.8/s
[progress] 16900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16900) elapsed=0.4s rate=46246.7/s
[progress] 17000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17000) elapsed=0.4s rate=46303.4/s
[progress] 17100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17100) elapsed=0.4s rate=46233.6/s
[chrom] chr20 done in 0.0s
[chrom] starting chr21
[progress] 17200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17200) elapsed=0.4s rate=46276.6/s
[progress] 17300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17300) elapsed=0.4s rate=46347.7/s
[chrom] chr21 done in 0.0s
[chrom] starting chr22
[progress] 17400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17400) elapsed=0.4s rate=46396.1/s
[progress] 17500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17500) elapsed=0.4s rate=46445.8/s
[progress] 17600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17600) elapsed=0.4s rate=46371.9/s
[progress] 17700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17700) elapsed=0.4s rate=46416.8/s
[chrom] chr22 done in 0.0s
[chrom] starting chrX
[progress] 17800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17800) elapsed=0.4s rate=46467.7/s
[progress] 17900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17900) elapsed=0.4s rate=46544.1/s
[progress] 18000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18000) elapsed=0.4s rate=46596.8/s
[progress] 18100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18100) elapsed=0.4s rate=46672.9/s
[progress] 18200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18200) elapsed=0.4s rate=46743.3/s
[progress] 18300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18300) elapsed=0.4s rate=46788.3/s
[progress] 18400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18400) elapsed=0.4s rate=46876.0/s
[progress] 18500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18500) elapsed=0.4s rate=46919.2/s
[progress] 18600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18600) elapsed=0.4s rate=46987.7/s
[chrom] chrX done in 0.0s
[done] 18683 variants in 0.4s (ok=0 no_reads=0 ref_mismatch=0 other=18683)