HG01361_x_HG01503_FF_5.log - Workflow Tracker

File Info

Filename: HG01361_x_HG01503_FF_5.log
Full Path: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/6a271842/logs/HG01361_x_HG01503_FF_5.log
Size: 32.0 KB
Workflow Run: adaptive-alpha-features-6a271842
Published: Jun 08, 2026 12:31 PM
Content

[init] ff = 0.050
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG01361_x_HG01503_FF_5.mix.bam
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 29095 sites
[chrom] starting chr1
[progress] 100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=100) elapsed=0.0s rate=37039.1/s
[progress] 200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=200) elapsed=0.0s rate=38197.8/s
[progress] 300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=300) elapsed=0.0s rate=36178.6/s
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[progress] 1300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1300) elapsed=0.0s rate=46092.0/s
[progress] 1400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1400) elapsed=0.0s rate=47035.3/s
[progress] 1500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1500) elapsed=0.0s rate=46826.8/s
[progress] 1600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1600) elapsed=0.0s rate=47581.8/s
[progress] 1700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1700) elapsed=0.0s rate=48302.5/s
[progress] 1800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1800) elapsed=0.0s rate=48744.5/s
[progress] 1900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1900) elapsed=0.0s rate=48600.3/s
[progress] 2000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2000) elapsed=0.0s rate=48895.2/s
[progress] 2100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2100) elapsed=0.0s rate=49289.0/s
[progress] 2200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2200) elapsed=0.0s rate=48181.4/s
[progress] 2300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2300) elapsed=0.0s rate=48016.0/s
[progress] 2400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2400) elapsed=0.0s rate=48325.2/s
[progress] 2500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2500) elapsed=0.1s rate=48276.5/s
[progress] 2600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2600) elapsed=0.1s rate=47628.8/s
[progress] 2700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2700) elapsed=0.1s rate=47881.2/s
[progress] 2800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2800) elapsed=0.1s rate=47962.3/s
[chrom] chr1 done in 0.1s
[chrom] starting chr2
[progress] 2900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2900) elapsed=0.1s rate=48171.4/s
[progress] 3000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3000) elapsed=0.1s rate=46496.1/s
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[progress] 3200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3200) elapsed=0.1s rate=46813.7/s
[progress] 3300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3300) elapsed=0.1s rate=47144.3/s
[progress] 3400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3400) elapsed=0.1s rate=47421.5/s
[progress] 3500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3500) elapsed=0.1s rate=47018.9/s
[progress] 3600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3600) elapsed=0.1s rate=47096.1/s
[progress] 3700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3700) elapsed=0.1s rate=47311.6/s
[progress] 3800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3800) elapsed=0.1s rate=47434.9/s
[progress] 3900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3900) elapsed=0.1s rate=46639.0/s
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[progress] 4100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4100) elapsed=0.1s rate=46917.3/s
[progress] 4200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4200) elapsed=0.1s rate=47015.3/s
[chrom] chr2 done in 0.0s
[chrom] starting chr3
[progress] 4300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4300) elapsed=0.1s rate=46645.8/s
[progress] 4400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4400) elapsed=0.1s rate=46904.1/s
[progress] 4500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4500) elapsed=0.1s rate=47098.7/s
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[progress] 4700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4700) elapsed=0.1s rate=47547.5/s
[progress] 4800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4800) elapsed=0.1s rate=47345.6/s
[progress] 4900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4900) elapsed=0.1s rate=47591.0/s
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[progress] 5800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5800) elapsed=0.1s rate=48048.0/s
[chrom] chr3 done in 0.0s
[chrom] starting chr4
[progress] 5900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5900) elapsed=0.1s rate=48263.9/s
[progress] 6000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6000) elapsed=0.1s rate=48451.4/s
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[progress] 6600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6600) elapsed=0.1s rate=49033.2/s
[progress] 6700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6700) elapsed=0.1s rate=48829.0/s
[chrom] chr4 done in 0.0s
[chrom] starting chr5
[progress] 6800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6800) elapsed=0.1s rate=48829.5/s
[progress] 6900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6900) elapsed=0.1s rate=48931.9/s
[progress] 7000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7000) elapsed=0.1s rate=48983.9/s
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[progress] 7300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7300) elapsed=0.1s rate=48771.7/s
[progress] 7400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7400) elapsed=0.2s rate=48869.5/s
[progress] 7500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7500) elapsed=0.2s rate=48743.2/s
[progress] 7600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7600) elapsed=0.2s rate=48834.9/s
[chrom] chr5 done in 0.0s
[chrom] starting chr6
[progress] 7700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7700) elapsed=0.2s rate=48970.2/s
[progress] 7800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7800) elapsed=0.2s rate=49072.4/s
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[progress] 8000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8000) elapsed=0.2s rate=49080.7/s
[progress] 8100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8100) elapsed=0.2s rate=49237.6/s
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[progress] 8300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8300) elapsed=0.2s rate=49435.6/s
[progress] 8400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8400) elapsed=0.2s rate=49478.6/s
[progress] 8500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8500) elapsed=0.2s rate=49291.3/s
[progress] 8600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8600) elapsed=0.2s rate=49396.4/s
[progress] 8700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8700) elapsed=0.2s rate=49409.6/s
[progress] 8800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8800) elapsed=0.2s rate=49520.8/s
[progress] 8900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8900) elapsed=0.2s rate=49398.2/s
[progress] 9000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9000) elapsed=0.2s rate=49514.7/s
[chrom] chr6 done in 0.0s
[chrom] starting chr7
[progress] 9100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9100) elapsed=0.2s rate=49536.8/s
[progress] 9200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9200) elapsed=0.2s rate=49648.4/s
[progress] 9300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9300) elapsed=0.2s rate=49716.8/s
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[progress] 9600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9600) elapsed=0.2s rate=49740.5/s
[progress] 9700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9700) elapsed=0.2s rate=49809.9/s
[progress] 9800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9800) elapsed=0.2s rate=49896.7/s
[progress] 9900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9900) elapsed=0.2s rate=49794.8/s
[progress] 10000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10000) elapsed=0.2s rate=49736.5/s
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[progress] 10700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10700) elapsed=0.2s rate=49948.9/s
[progress] 10800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10800) elapsed=0.2s rate=49896.4/s
[chrom] chr7 done in 0.0s
[chrom] starting chr8
[progress] 10900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10900) elapsed=0.2s rate=49975.7/s
[progress] 11000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11000) elapsed=0.2s rate=49980.2/s
[progress] 11100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11100) elapsed=0.2s rate=50068.7/s
[progress] 11200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11200) elapsed=0.2s rate=50149.2/s
[progress] 11300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11300) elapsed=0.2s rate=49973.7/s
[progress] 11400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11400) elapsed=0.2s rate=50070.2/s
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[progress] 11600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11600) elapsed=0.2s rate=50276.0/s
[chrom] chr8 done in 0.0s
[chrom] starting chr9
[progress] 11700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11700) elapsed=0.2s rate=50394.2/s
[progress] 11800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11800) elapsed=0.2s rate=50237.2/s
[progress] 11900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11900) elapsed=0.2s rate=50289.5/s
[progress] 12000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12000) elapsed=0.2s rate=50319.0/s
[progress] 12100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12100) elapsed=0.2s rate=50367.7/s
[progress] 12200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12200) elapsed=0.2s rate=50281.3/s
[progress] 12300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12300) elapsed=0.2s rate=50330.0/s
[progress] 12400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12400) elapsed=0.2s rate=50361.6/s
[progress] 12500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12500) elapsed=0.2s rate=50404.5/s
[progress] 12600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12600) elapsed=0.2s rate=50461.4/s
[chrom] chr9 done in 0.0s
[chrom] starting chr10
[progress] 12700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12700) elapsed=0.3s rate=50360.2/s
[progress] 12800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12800) elapsed=0.3s rate=50411.0/s
[progress] 12900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12900) elapsed=0.3s rate=50447.6/s
[progress] 13000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13000) elapsed=0.3s rate=50449.8/s
[progress] 13100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13100) elapsed=0.3s rate=50358.5/s
[progress] 13200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13200) elapsed=0.3s rate=50433.2/s
[progress] 13300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13300) elapsed=0.3s rate=50487.1/s
[chrom] chr10 done in 0.0s
[chrom] starting chr11
[progress] 13400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13400) elapsed=0.3s rate=50540.6/s
[progress] 13500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13500) elapsed=0.3s rate=50555.6/s
[progress] 13600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13600) elapsed=0.3s rate=50484.4/s
[progress] 13700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13700) elapsed=0.3s rate=50602.4/s
[progress] 13800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13800) elapsed=0.3s rate=50690.4/s
[progress] 13900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13900) elapsed=0.3s rate=50783.5/s
[progress] 14000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14000) elapsed=0.3s rate=50833.4/s
[progress] 14100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14100) elapsed=0.3s rate=50704.8/s
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[progress] 14700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14700) elapsed=0.3s rate=50845.7/s
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[progress] 14900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14900) elapsed=0.3s rate=50955.9/s
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[progress] 15300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15300) elapsed=0.3s rate=50965.4/s
[chrom] chr11 done in 0.0s
[chrom] starting chr12
[progress] 15400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15400) elapsed=0.3s rate=50969.5/s
[progress] 15500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15500) elapsed=0.3s rate=50876.9/s
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[progress] 15900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15900) elapsed=0.3s rate=50990.4/s
[progress] 16000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16000) elapsed=0.3s rate=50929.6/s
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[progress] 16400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16400) elapsed=0.3s rate=50906.2/s
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[progress] 16600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16600) elapsed=0.3s rate=51014.0/s
[chrom] chr12 done in 0.0s
[chrom] starting chr13
[progress] 16700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16700) elapsed=0.3s rate=51040.6/s
[progress] 16800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16800) elapsed=0.3s rate=51055.2/s
[progress] 16900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16900) elapsed=0.3s rate=50989.8/s
[chrom] chr13 done in 0.0s
[chrom] starting chr14
[progress] 17000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17000) elapsed=0.3s rate=51012.2/s
[progress] 17100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17100) elapsed=0.3s rate=51063.6/s
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[progress] 17400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17400) elapsed=0.3s rate=51085.2/s
[progress] 17500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17500) elapsed=0.3s rate=51145.6/s
[progress] 17600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17600) elapsed=0.3s rate=51193.6/s
[progress] 17700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17700) elapsed=0.3s rate=51279.7/s
[progress] 17800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17800) elapsed=0.3s rate=51349.0/s
[progress] 17900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17900) elapsed=0.3s rate=51433.1/s
[chrom] chr14 done in 0.0s
[chrom] starting chr15
[progress] 18000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18000) elapsed=0.4s rate=51379.8/s
[progress] 18100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18100) elapsed=0.4s rate=51361.3/s
[progress] 18200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18200) elapsed=0.4s rate=51401.8/s
[progress] 18300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18300) elapsed=0.4s rate=51417.1/s
[progress] 18400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18400) elapsed=0.4s rate=51331.8/s
[progress] 18500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18500) elapsed=0.4s rate=51339.7/s
[progress] 18600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18600) elapsed=0.4s rate=51358.6/s
[chrom] chr15 done in 0.0s
[chrom] starting chr16
[progress] 18700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18700) elapsed=0.4s rate=51369.1/s
[progress] 18800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18800) elapsed=0.4s rate=51425.4/s
[progress] 18900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18900) elapsed=0.4s rate=51340.3/s
[progress] 19000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19000) elapsed=0.4s rate=51384.1/s
[progress] 19100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19100) elapsed=0.4s rate=51438.0/s
[progress] 19200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19200) elapsed=0.4s rate=51505.7/s
[progress] 19300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19300) elapsed=0.4s rate=51583.2/s
[progress] 19400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19400) elapsed=0.4s rate=51640.8/s
[progress] 19500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19500) elapsed=0.4s rate=51527.5/s
[progress] 19600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19600) elapsed=0.4s rate=51545.6/s
[progress] 19700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19700) elapsed=0.4s rate=51573.3/s
[progress] 19800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19800) elapsed=0.4s rate=51577.4/s
[progress] 19900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19900) elapsed=0.4s rate=51522.0/s
[chrom] chr16 done in 0.0s
[chrom] starting chr17
[progress] 20000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20000) elapsed=0.4s rate=51556.1/s
[progress] 20100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20100) elapsed=0.4s rate=51598.9/s
[progress] 20200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20200) elapsed=0.4s rate=51649.4/s
[progress] 20300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20300) elapsed=0.4s rate=51698.0/s
[progress] 20400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20400) elapsed=0.4s rate=51634.3/s
[progress] 20500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20500) elapsed=0.4s rate=51636.1/s
[progress] 20600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20600) elapsed=0.4s rate=51681.4/s
[progress] 20700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20700) elapsed=0.4s rate=51703.6/s
[progress] 20800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20800) elapsed=0.4s rate=51751.1/s
[progress] 20900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20900) elapsed=0.4s rate=51696.5/s
[progress] 21000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21000) elapsed=0.4s rate=51706.2/s
[progress] 21100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21100) elapsed=0.4s rate=51733.3/s
[progress] 21200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21200) elapsed=0.4s rate=51767.3/s
[progress] 21300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21300) elapsed=0.4s rate=51784.0/s
[progress] 21400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21400) elapsed=0.4s rate=51700.7/s
[progress] 21500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21500) elapsed=0.4s rate=51729.7/s
[chrom] chr17 done in 0.0s
[chrom] starting chr18
[progress] 21600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21600) elapsed=0.4s rate=51748.4/s
[progress] 21700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21700) elapsed=0.4s rate=51772.2/s
[progress] 21800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21800) elapsed=0.4s rate=51706.0/s
[chrom] chr18 done in 0.0s
[chrom] starting chr19
[progress] 21900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21900) elapsed=0.4s rate=51715.2/s
[progress] 22000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22000) elapsed=0.4s rate=51745.7/s
[progress] 22100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22100) elapsed=0.4s rate=51770.4/s
[progress] 22200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22200) elapsed=0.4s rate=51800.7/s
[progress] 22300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22300) elapsed=0.4s rate=51711.4/s
[progress] 22400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22400) elapsed=0.4s rate=51753.7/s
[progress] 22500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22500) elapsed=0.4s rate=51800.7/s
[progress] 22600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22600) elapsed=0.4s rate=51837.6/s
[progress] 22700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22700) elapsed=0.4s rate=51885.3/s
[progress] 22800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22800) elapsed=0.4s rate=51935.0/s
[progress] 22900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22900) elapsed=0.4s rate=51857.7/s
[progress] 23000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23000) elapsed=0.4s rate=51906.9/s
[progress] 23100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23100) elapsed=0.4s rate=51958.9/s
[progress] 23200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23200) elapsed=0.4s rate=52003.6/s
[progress] 23300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23300) elapsed=0.4s rate=52065.8/s
[progress] 23400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23400) elapsed=0.4s rate=52125.0/s
[progress] 23500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23500) elapsed=0.5s rate=52181.8/s
[progress] 23600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23600) elapsed=0.5s rate=52168.9/s
[progress] 23700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23700) elapsed=0.5s rate=52216.1/s
[progress] 23800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23800) elapsed=0.5s rate=52262.5/s
[progress] 23900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23900) elapsed=0.5s rate=52279.3/s
[progress] 24000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24000) elapsed=0.5s rate=52321.8/s
[progress] 24100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24100) elapsed=0.5s rate=52375.0/s
[progress] 24200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24200) elapsed=0.5s rate=52435.8/s
[progress] 24300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24300) elapsed=0.5s rate=52380.7/s
[progress] 24400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24400) elapsed=0.5s rate=52418.2/s
[progress] 24500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24500) elapsed=0.5s rate=52448.5/s
[progress] 24600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24600) elapsed=0.5s rate=52501.2/s
[progress] 24700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24700) elapsed=0.5s rate=52517.2/s
[progress] 24800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24800) elapsed=0.5s rate=52554.3/s
[progress] 24900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24900) elapsed=0.5s rate=52481.1/s
[progress] 25000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25000) elapsed=0.5s rate=52456.5/s
[progress] 25100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25100) elapsed=0.5s rate=52501.2/s
[progress] 25200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25200) elapsed=0.5s rate=52556.0/s
[progress] 25300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25300) elapsed=0.5s rate=52601.5/s
[progress] 25400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25400) elapsed=0.5s rate=52637.8/s
[progress] 25500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25500) elapsed=0.5s rate=52587.1/s
[progress] 25600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25600) elapsed=0.5s rate=52549.5/s
[progress] 25700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25700) elapsed=0.5s rate=52589.8/s
[progress] 25800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25800) elapsed=0.5s rate=52640.0/s
[progress] 25900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25900) elapsed=0.5s rate=52693.3/s
[progress] 26000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26000) elapsed=0.5s rate=52744.7/s
[progress] 26100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26100) elapsed=0.5s rate=52799.6/s
[chrom] chr19 done in 0.1s
[chrom] starting chr20
[progress] 26200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26200) elapsed=0.5s rate=52738.5/s
[progress] 26300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26300) elapsed=0.5s rate=52769.2/s
[progress] 26400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26400) elapsed=0.5s rate=52783.0/s
[progress] 26500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26500) elapsed=0.5s rate=52809.9/s
[progress] 26600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26600) elapsed=0.5s rate=52855.1/s
[progress] 26700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26700) elapsed=0.5s rate=52816.9/s
[chrom] chr20 done in 0.0s
[chrom] starting chr21
[progress] 26800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26800) elapsed=0.5s rate=52832.7/s
[progress] 26900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26900) elapsed=0.5s rate=52828.9/s
[progress] 27000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27000) elapsed=0.5s rate=52836.1/s
[chrom] chr21 done in 0.0s
[chrom] starting chr22
[progress] 27100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27100) elapsed=0.5s rate=52829.7/s
[progress] 27200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27200) elapsed=0.5s rate=52840.1/s
[progress] 27300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27300) elapsed=0.5s rate=52739.6/s
[progress] 27400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27400) elapsed=0.5s rate=52732.0/s
[progress] 27500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27500) elapsed=0.5s rate=52718.6/s
[progress] 27600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27600) elapsed=0.5s rate=52729.5/s
[progress] 27700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27700) elapsed=0.5s rate=52707.4/s
[chrom] chr22 done in 0.0s
[chrom] starting chrX
[progress] 27800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27800) elapsed=0.5s rate=52487.1/s
[progress] 27900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27900) elapsed=0.5s rate=52512.9/s
[progress] 28000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28000) elapsed=0.5s rate=52547.5/s
[progress] 28100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28100) elapsed=0.5s rate=52581.3/s
[progress] 28200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28200) elapsed=0.5s rate=52594.9/s
[progress] 28300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28300) elapsed=0.5s rate=52622.4/s
[progress] 28400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28400) elapsed=0.5s rate=52640.7/s
[progress] 28500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28500) elapsed=0.5s rate=52677.9/s
[progress] 28600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28600) elapsed=0.5s rate=52707.9/s
[progress] 28700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28700) elapsed=0.5s rate=52738.4/s
[progress] 28800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28800) elapsed=0.5s rate=52758.6/s
[progress] 28900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28900) elapsed=0.5s rate=52793.7/s
[progress] 29000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29000) elapsed=0.5s rate=52827.5/s
[chrom] chrX done in 0.0s
[done] 29097 variants in 0.6s (ok=0 no_reads=0 ref_mismatch=0 other=29097)