Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/targets/HG01109_x_HG01175_FF_10.targets.tsv
  Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/e87a2eb159529391d95109176b2bbf/HG01109_x_HG01175_FF_10.mix.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/2a76f5f06f4ac392e5f3ad5141a451/.command.sh
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/vcfs/HG01109_x_HG01175_FF_10.vcf
  Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/2a76f5f06f4ac392e5f3ad5141a451/.command.run
==> STAGING COMPLETE (7 inputs)

[init] ff = 0.100
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG01109_x_HG01175_FF_10.mix.bam
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 22074 sites
[chrom] starting chr1
[progress] 100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=100) elapsed=0.0s rate=26817.8/s
[progress] 200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=200) elapsed=0.0s rate=25370.8/s
[progress] 300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=300) elapsed=0.0s rate=31011.5/s
[progress] 400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=400) elapsed=0.0s rate=35617.4/s
[progress] 500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=500) elapsed=0.0s rate=35788.2/s
[progress] 600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=600) elapsed=0.0s rate=37563.7/s
[progress] 700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=700) elapsed=0.0s rate=40104.0/s
[progress] 800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=800) elapsed=0.0s rate=41444.7/s
[progress] 900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=900) elapsed=0.0s rate=42861.2/s
[progress] 1000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1000) elapsed=0.0s rate=41794.3/s
[progress] 1100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1100) elapsed=0.0s rate=42995.7/s
[progress] 1200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1200) elapsed=0.0s rate=44395.9/s
[progress] 1300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1300) elapsed=0.0s rate=45470.5/s
[progress] 1400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1400) elapsed=0.0s rate=46892.2/s
[progress] 1500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1500) elapsed=0.0s rate=47857.6/s
[progress] 1600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1600) elapsed=0.0s rate=48051.9/s
[progress] 1700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1700) elapsed=0.0s rate=48527.7/s
[progress] 1800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1800) elapsed=0.0s rate=48957.6/s
[progress] 1900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1900) elapsed=0.0s rate=49427.1/s
[progress] 2000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2000) elapsed=0.0s rate=49670.5/s
[progress] 2100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2100) elapsed=0.0s rate=48055.7/s
[progress] 2200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2200) elapsed=0.0s rate=48362.5/s
[chrom] chr1 done in 0.0s
[chrom] starting chr2
[progress] 2300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2300) elapsed=0.0s rate=48445.2/s
[progress] 2400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2400) elapsed=0.0s rate=48897.7/s
[progress] 2500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2500) elapsed=0.1s rate=48105.1/s
[progress] 2600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2600) elapsed=0.1s rate=48606.9/s
[progress] 2700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2700) elapsed=0.1s rate=48836.8/s
[progress] 2800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2800) elapsed=0.1s rate=49137.9/s
[progress] 2900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2900) elapsed=0.1s rate=48375.9/s
[progress] 3000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3000) elapsed=0.1s rate=48528.3/s
[progress] 3100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3100) elapsed=0.1s rate=48749.8/s
[progress] 3200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3200) elapsed=0.1s rate=48983.9/s
[progress] 3300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3300) elapsed=0.1s rate=48345.8/s
[progress] 3400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3400) elapsed=0.1s rate=48531.8/s
[chrom] chr2 done in 0.0s
[chrom] starting chr3
[progress] 3500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3500) elapsed=0.1s rate=48794.2/s
[progress] 3600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3600) elapsed=0.1s rate=49029.4/s
[progress] 3700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3700) elapsed=0.1s rate=49226.4/s
[progress] 3800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3800) elapsed=0.1s rate=49541.5/s
[progress] 3900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3900) elapsed=0.1s rate=49010.0/s
[progress] 4000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4000) elapsed=0.1s rate=49103.0/s
[progress] 4100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4100) elapsed=0.1s rate=49237.1/s
[progress] 4200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4200) elapsed=0.1s rate=49217.4/s
[progress] 4300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4300) elapsed=0.1s rate=48523.2/s
[progress] 4400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4400) elapsed=0.1s rate=48458.1/s
[progress] 4500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4500) elapsed=0.1s rate=48454.2/s
[chrom] chr3 done in 0.0s
[chrom] starting chr4
[progress] 4600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4600) elapsed=0.1s rate=48320.7/s
[progress] 4700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4700) elapsed=0.1s rate=47662.1/s
[progress] 4800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4800) elapsed=0.1s rate=47633.3/s
[progress] 4900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4900) elapsed=0.1s rate=47561.3/s
[progress] 5000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5000) elapsed=0.1s rate=47552.7/s
[progress] 5100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5100) elapsed=0.1s rate=47425.4/s
[progress] 5200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5200) elapsed=0.1s rate=46666.1/s
[chrom] chr4 done in 0.0s
[chrom] starting chr5
[progress] 5300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5300) elapsed=0.1s rate=46678.3/s
[progress] 5400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5400) elapsed=0.1s rate=46575.7/s
[progress] 5500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5500) elapsed=0.1s rate=46512.0/s
[progress] 5600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5600) elapsed=0.1s rate=45873.4/s
[progress] 5700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5700) elapsed=0.1s rate=45940.6/s
[progress] 5800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5800) elapsed=0.1s rate=45978.2/s
[progress] 5900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5900) elapsed=0.1s rate=46042.2/s
[progress] 6000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6000) elapsed=0.1s rate=46100.2/s
[chrom] chr5 done in 0.0s
[chrom] starting chr6
[progress] 6100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6100) elapsed=0.1s rate=45608.5/s
[progress] 6200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6200) elapsed=0.1s rate=45547.7/s
[progress] 6300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6300) elapsed=0.1s rate=45689.3/s
[progress] 6400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6400) elapsed=0.1s rate=45800.0/s
[progress] 6500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6500) elapsed=0.1s rate=45813.7/s
[progress] 6600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6600) elapsed=0.1s rate=45289.5/s
[progress] 6700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6700) elapsed=0.1s rate=45326.6/s
[progress] 6800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6800) elapsed=0.1s rate=45343.1/s
[progress] 6900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6900) elapsed=0.2s rate=45313.0/s
[progress] 7000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7000) elapsed=0.2s rate=44817.5/s
[progress] 7100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7100) elapsed=0.2s rate=44847.2/s
[chrom] chr6 done in 0.0s
[chrom] starting chr7
[progress] 7200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7200) elapsed=0.2s rate=44875.7/s
[progress] 7300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7300) elapsed=0.2s rate=44924.1/s
[progress] 7400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7400) elapsed=0.2s rate=45046.0/s
[progress] 7500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7500) elapsed=0.2s rate=44615.5/s
[progress] 7600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7600) elapsed=0.2s rate=44677.2/s
[progress] 7700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7700) elapsed=0.2s rate=44696.9/s
[progress] 7800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7800) elapsed=0.2s rate=44722.7/s
[progress] 7900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7900) elapsed=0.2s rate=44225.8/s
[progress] 8000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8000) elapsed=0.2s rate=44245.9/s
[progress] 8100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8100) elapsed=0.2s rate=44330.0/s
[progress] 8200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8200) elapsed=0.2s rate=44272.0/s
[progress] 8300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8300) elapsed=0.2s rate=43993.6/s
[progress] 8400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8400) elapsed=0.2s rate=44194.8/s
[progress] 8500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8500) elapsed=0.2s rate=44340.1/s
[chrom] chr7 done in 0.0s
[chrom] starting chr8
[progress] 8600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8600) elapsed=0.2s rate=44467.0/s
[progress] 8700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8700) elapsed=0.2s rate=44604.4/s
[progress] 8800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8800) elapsed=0.2s rate=44747.6/s
[progress] 8900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8900) elapsed=0.2s rate=44478.1/s
[progress] 9000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9000) elapsed=0.2s rate=44640.3/s
[progress] 9100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9100) elapsed=0.2s rate=44777.9/s
[chrom] chr8 done in 0.0s
[chrom] starting chr9
[progress] 9200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9200) elapsed=0.2s rate=44893.5/s
[progress] 9300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9300) elapsed=0.2s rate=44736.3/s
[progress] 9400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9400) elapsed=0.2s rate=44836.4/s
[progress] 9500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9500) elapsed=0.2s rate=44954.4/s
[progress] 9600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9600) elapsed=0.2s rate=45056.9/s
[progress] 9700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9700) elapsed=0.2s rate=45163.6/s
[progress] 9800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9800) elapsed=0.2s rate=44985.7/s
[chrom] chr9 done in 0.0s
[chrom] starting chr10
[progress] 9900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9900) elapsed=0.2s rate=45080.5/s
[progress] 10000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10000) elapsed=0.2s rate=45141.5/s
[progress] 10100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10100) elapsed=0.2s rate=45223.9/s
[progress] 10200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10200) elapsed=0.2s rate=45078.5/s
[progress] 10300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10300) elapsed=0.2s rate=45166.6/s
[progress] 10400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10400) elapsed=0.2s rate=45289.1/s
[progress] 10500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10500) elapsed=0.2s rate=45405.2/s
[chrom] chr10 done in 0.0s
[chrom] starting chr11
[progress] 10600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10600) elapsed=0.2s rate=45473.7/s
[progress] 10700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10700) elapsed=0.2s rate=45394.0/s
[progress] 10800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10800) elapsed=0.2s rate=45522.6/s
[progress] 10900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10900) elapsed=0.2s rate=45628.6/s
[progress] 11000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11000) elapsed=0.2s rate=45670.1/s
[progress] 11100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11100) elapsed=0.2s rate=45760.3/s
[progress] 11200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11200) elapsed=0.2s rate=45568.2/s
[progress] 11300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11300) elapsed=0.2s rate=45629.8/s
[progress] 11400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11400) elapsed=0.2s rate=45734.5/s
[progress] 11500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11500) elapsed=0.3s rate=45868.3/s
[progress] 11600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11600) elapsed=0.3s rate=45963.5/s
[progress] 11700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11700) elapsed=0.3s rate=45869.5/s
[progress] 11800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11800) elapsed=0.3s rate=45969.0/s
[progress] 11900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11900) elapsed=0.3s rate=46046.6/s
[progress] 12000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12000) elapsed=0.3s rate=46126.7/s
[progress] 12100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12100) elapsed=0.3s rate=46192.8/s
[chrom] chr11 done in 0.0s
[chrom] starting chr12
[progress] 12200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12200) elapsed=0.3s rate=46008.6/s
[progress] 12300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12300) elapsed=0.3s rate=46013.8/s
[progress] 12400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12400) elapsed=0.3s rate=46112.1/s
[progress] 12500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12500) elapsed=0.3s rate=46208.9/s
[progress] 12600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12600) elapsed=0.3s rate=46123.7/s
[progress] 12700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12700) elapsed=0.3s rate=46205.5/s
[progress] 12800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12800) elapsed=0.3s rate=46328.7/s
[progress] 12900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12900) elapsed=0.3s rate=46373.0/s
[progress] 13000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13000) elapsed=0.3s rate=46413.8/s
[progress] 13100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13100) elapsed=0.3s rate=46314.4/s
[chrom] chr12 done in 0.0s
[chrom] starting chr13
[progress] 13200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13200) elapsed=0.3s rate=46414.3/s
[progress] 13300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13300) elapsed=0.3s rate=46468.0/s
[progress] 13400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13400) elapsed=0.3s rate=46554.2/s
[chrom] chr13 done in 0.0s
[chrom] starting chr14
[progress] 13500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13500) elapsed=0.3s rate=46619.8/s
[progress] 13600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13600) elapsed=0.3s rate=46454.5/s
[progress] 13700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13700) elapsed=0.3s rate=46476.1/s
[progress] 13800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13800) elapsed=0.3s rate=46544.5/s
[progress] 13900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13900) elapsed=0.3s rate=46627.2/s
[progress] 14000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14000) elapsed=0.3s rate=46565.0/s
[chrom] chr14 done in 0.0s
[chrom] starting chr15
[progress] 14100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14100) elapsed=0.3s rate=46660.1/s
[progress] 14200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14200) elapsed=0.3s rate=46727.4/s
[progress] 14300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14300) elapsed=0.3s rate=46783.0/s
[progress] 14400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14400) elapsed=0.3s rate=46618.1/s
[progress] 14500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14500) elapsed=0.3s rate=46676.6/s
[chrom] chr15 done in 0.0s
[chrom] starting chr16
[progress] 14600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14600) elapsed=0.3s rate=46711.6/s
[progress] 14700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14700) elapsed=0.3s rate=46763.6/s
[progress] 14800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14800) elapsed=0.3s rate=46847.7/s
[progress] 14900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14900) elapsed=0.3s rate=46705.9/s
[progress] 15000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15000) elapsed=0.3s rate=46790.6/s
[progress] 15100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15100) elapsed=0.3s rate=46897.8/s
[progress] 15200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15200) elapsed=0.3s rate=46973.6/s
[progress] 15300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15300) elapsed=0.3s rate=47071.2/s
[progress] 15400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15400) elapsed=0.3s rate=46959.5/s
[progress] 15500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15500) elapsed=0.3s rate=47021.0/s
[chrom] chr16 done in 0.0s
[chrom] starting chr17
[progress] 15600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15600) elapsed=0.3s rate=47090.9/s
[progress] 15700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15700) elapsed=0.3s rate=47152.5/s
[progress] 15800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15800) elapsed=0.3s rate=47252.2/s
[progress] 15900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15900) elapsed=0.3s rate=47325.8/s
[progress] 16000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16000) elapsed=0.3s rate=47209.1/s
[progress] 16100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16100) elapsed=0.3s rate=47269.1/s
[progress] 16200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16200) elapsed=0.3s rate=47321.5/s
[progress] 16300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16300) elapsed=0.3s rate=47408.5/s
[progress] 16400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16400) elapsed=0.3s rate=47284.9/s
[progress] 16500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16500) elapsed=0.3s rate=47347.2/s
[progress] 16600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16600) elapsed=0.4s rate=47422.6/s
[progress] 16700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16700) elapsed=0.4s rate=47389.7/s
[progress] 16800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16800) elapsed=0.4s rate=47422.1/s
[progress] 16900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16900) elapsed=0.4s rate=47472.6/s
[chrom] chr17 done in 0.0s
[chrom] starting chr18
[progress] 17000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17000) elapsed=0.4s rate=47379.9/s
[progress] 17100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17100) elapsed=0.4s rate=47409.0/s
[chrom] chr18 done in 0.0s
[chrom] starting chr19
[progress] 17200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17200) elapsed=0.4s rate=47436.6/s
[progress] 17300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17300) elapsed=0.4s rate=47464.8/s
[progress] 17400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17400) elapsed=0.4s rate=47318.5/s
[progress] 17500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17500) elapsed=0.4s rate=47333.9/s
[progress] 17600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17600) elapsed=0.4s rate=47394.0/s
[progress] 17700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17700) elapsed=0.4s rate=47472.7/s
[progress] 17800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17800) elapsed=0.4s rate=47559.7/s
[progress] 17900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17900) elapsed=0.4s rate=47464.1/s
[progress] 18000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18000) elapsed=0.4s rate=47486.9/s
[progress] 18100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18100) elapsed=0.4s rate=47549.1/s
[progress] 18200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18200) elapsed=0.4s rate=47633.8/s
[progress] 18300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18300) elapsed=0.4s rate=47692.0/s
[progress] 18400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18400) elapsed=0.4s rate=47727.0/s
[progress] 18500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18500) elapsed=0.4s rate=47650.1/s
[progress] 18600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18600) elapsed=0.4s rate=47704.0/s
[progress] 18700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18700) elapsed=0.4s rate=47739.7/s
[progress] 18800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18800) elapsed=0.4s rate=47773.4/s
[progress] 18900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18900) elapsed=0.4s rate=47798.0/s
[progress] 19000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19000) elapsed=0.4s rate=47851.3/s
[progress] 19100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19100) elapsed=0.4s rate=47803.1/s
[progress] 19200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19200) elapsed=0.4s rate=47850.7/s
[progress] 19300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19300) elapsed=0.4s rate=47892.5/s
[progress] 19400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19400) elapsed=0.4s rate=47973.0/s
[progress] 19500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19500) elapsed=0.4s rate=48050.5/s
[progress] 19600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19600) elapsed=0.4s rate=48117.2/s
[progress] 19700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19700) elapsed=0.4s rate=47986.3/s
[progress] 19800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19800) elapsed=0.4s rate=48025.9/s
[progress] 19900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19900) elapsed=0.4s rate=48093.1/s
[progress] 20000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20000) elapsed=0.4s rate=48140.3/s
[chrom] chr19 done in 0.1s
[chrom] starting chr20
[progress] 20100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20100) elapsed=0.4s rate=48176.1/s
[progress] 20200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20200) elapsed=0.4s rate=48124.2/s
[progress] 20300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20300) elapsed=0.4s rate=48180.8/s
[progress] 20400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20400) elapsed=0.4s rate=48235.4/s
[progress] 20500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20500) elapsed=0.4s rate=48289.0/s
[progress] 20600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20600) elapsed=0.4s rate=48318.9/s
[chrom] chr20 done in 0.0s
[chrom] starting chr21
[progress] 20700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20700) elapsed=0.4s rate=48233.1/s
[progress] 20800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20800) elapsed=0.4s rate=48282.3/s
[chrom] chr21 done in 0.0s
[chrom] starting chr22
[progress] 20900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20900) elapsed=0.4s rate=48314.5/s
[progress] 21000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21000) elapsed=0.4s rate=48355.9/s
[progress] 21100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21100) elapsed=0.4s rate=48407.9/s
[progress] 21200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21200) elapsed=0.4s rate=48454.3/s
[progress] 21300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21300) elapsed=0.4s rate=48412.5/s
[progress] 21400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21400) elapsed=0.4s rate=48445.4/s
[chrom] chr22 done in 0.0s
[chrom] starting chrX
[progress] 21500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21500) elapsed=0.4s rate=48470.0/s
[progress] 21600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21600) elapsed=0.4s rate=48503.7/s
[progress] 21700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21700) elapsed=0.4s rate=48541.6/s
[progress] 21800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21800) elapsed=0.4s rate=48578.2/s
[progress] 21900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21900) elapsed=0.5s rate=48634.9/s
[progress] 22000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22000) elapsed=0.5s rate=48654.8/s
[chrom] chrX done in 0.0s
[done] 22076 variants in 0.5s (ok=0 no_reads=0 ref_mismatch=0 other=22076)