HG00733_x_HG00735_FF_5.log - Workflow Tracker

File Info

Filename: HG00733_x_HG00735_FF_5.log
Full Path: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/6a271842/logs/HG00733_x_HG00735_FF_5.log
Size: 30.5 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 HG00733_x_HG00735_FF_5.mix.bam
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 27622 sites
[chrom] starting chr1
[progress] 100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=100) elapsed=0.0s rate=38116.2/s
[progress] 200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=200) elapsed=0.0s rate=39647.5/s
[progress] 300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=300) elapsed=0.0s rate=37854.7/s
[progress] 400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=400) elapsed=0.0s rate=40436.8/s
[progress] 500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=500) elapsed=0.0s rate=42975.3/s
[progress] 600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=600) elapsed=0.0s rate=43081.1/s
[progress] 700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=700) elapsed=0.0s rate=45098.0/s
[progress] 800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=800) elapsed=0.0s rate=46383.7/s
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[progress] 1200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1200) elapsed=0.0s rate=47891.6/s
[progress] 1300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1300) elapsed=0.0s rate=48477.4/s
[progress] 1400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1400) elapsed=0.0s rate=48813.5/s
[progress] 1500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1500) elapsed=0.0s rate=49855.0/s
[progress] 1600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1600) elapsed=0.0s rate=50899.0/s
[progress] 1700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1700) elapsed=0.0s rate=50152.4/s
[progress] 1800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1800) elapsed=0.0s rate=50938.2/s
[progress] 1900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1900) elapsed=0.0s rate=51385.9/s
[progress] 2000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2000) elapsed=0.0s rate=51435.5/s
[progress] 2100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2100) elapsed=0.0s rate=51625.8/s
[progress] 2200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2200) elapsed=0.0s rate=50814.9/s
[progress] 2300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2300) elapsed=0.0s rate=51079.6/s
[progress] 2400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2400) elapsed=0.0s rate=51435.7/s
[progress] 2500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2500) elapsed=0.0s rate=51589.9/s
[progress] 2600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2600) elapsed=0.1s rate=50732.7/s
[progress] 2700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2700) elapsed=0.1s rate=50724.4/s
[progress] 2800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2800) elapsed=0.1s rate=50885.2/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=51167.9/s
[progress] 3000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3000) elapsed=0.1s rate=51300.4/s
[progress] 3100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3100) elapsed=0.1s rate=50670.3/s
[progress] 3200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3200) elapsed=0.1s rate=50811.2/s
[progress] 3300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3300) elapsed=0.1s rate=51108.9/s
[progress] 3400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3400) elapsed=0.1s rate=51207.9/s
[progress] 3500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3500) elapsed=0.1s rate=51338.0/s
[progress] 3600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3600) elapsed=0.1s rate=50448.4/s
[progress] 3700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3700) elapsed=0.1s rate=50524.6/s
[progress] 3800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3800) elapsed=0.1s rate=50685.5/s
[progress] 3900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3900) elapsed=0.1s rate=50675.9/s
[progress] 4000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4000) elapsed=0.1s rate=50225.5/s
[progress] 4100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4100) elapsed=0.1s rate=50292.7/s
[progress] 4200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4200) elapsed=0.1s rate=50388.5/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=50474.4/s
[progress] 4400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4400) elapsed=0.1s rate=50031.1/s
[progress] 4500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4500) elapsed=0.1s rate=50141.4/s
[progress] 4600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4600) elapsed=0.1s rate=50331.3/s
[progress] 4700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4700) elapsed=0.1s rate=49921.4/s
[progress] 4800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4800) elapsed=0.1s rate=50017.9/s
[progress] 4900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4900) elapsed=0.1s rate=49573.5/s
[progress] 5000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5000) elapsed=0.1s rate=49639.4/s
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[progress] 5300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5300) elapsed=0.1s rate=49355.7/s
[progress] 5400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5400) elapsed=0.1s rate=49538.2/s
[progress] 5500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5500) elapsed=0.1s rate=49716.1/s
[chrom] chr3 done in 0.0s
[chrom] starting chr4
[progress] 5600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5600) elapsed=0.1s rate=49966.0/s
[progress] 5700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5700) elapsed=0.1s rate=50074.0/s
[progress] 5800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5800) elapsed=0.1s rate=49756.4/s
[progress] 5900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5900) elapsed=0.1s rate=49833.9/s
[progress] 6000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6000) elapsed=0.1s rate=50022.8/s
[progress] 6100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6100) elapsed=0.1s rate=50251.8/s
[progress] 6200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6200) elapsed=0.1s rate=49800.3/s
[progress] 6300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6300) elapsed=0.1s rate=49893.7/s
[chrom] chr4 done in 0.0s
[chrom] starting chr5
[progress] 6400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6400) elapsed=0.1s rate=49942.3/s
[progress] 6500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6500) elapsed=0.1s rate=49973.1/s
[progress] 6600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6600) elapsed=0.1s rate=49820.8/s
[progress] 6700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6700) elapsed=0.1s rate=49854.9/s
[progress] 6800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6800) elapsed=0.1s rate=49918.6/s
[progress] 6900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6900) elapsed=0.1s rate=49994.7/s
[progress] 7000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7000) elapsed=0.1s rate=50125.9/s
[progress] 7100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7100) elapsed=0.1s rate=49865.1/s
[progress] 7200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7200) elapsed=0.1s rate=49961.3/s
[chrom] chr5 done in 0.0s
[chrom] starting chr6
[progress] 7300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7300) elapsed=0.1s rate=50095.4/s
[progress] 7400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7400) elapsed=0.1s rate=50168.3/s
[progress] 7500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7500) elapsed=0.1s rate=50264.4/s
[progress] 7600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7600) elapsed=0.2s rate=50091.0/s
[progress] 7700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7700) elapsed=0.2s rate=50283.0/s
[progress] 7800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7800) elapsed=0.2s rate=50361.5/s
[progress] 7900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7900) elapsed=0.2s rate=50479.3/s
[progress] 8000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8000) elapsed=0.2s rate=50525.6/s
[progress] 8100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8100) elapsed=0.2s rate=50331.0/s
[progress] 8200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8200) elapsed=0.2s rate=50354.1/s
[progress] 8300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8300) elapsed=0.2s rate=50393.6/s
[progress] 8400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8400) elapsed=0.2s rate=50455.2/s
[progress] 8500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8500) elapsed=0.2s rate=50246.3/s
[chrom] chr6 done in 0.0s
[chrom] starting chr7
[progress] 8600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8600) elapsed=0.2s rate=50273.6/s
[progress] 8700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8700) elapsed=0.2s rate=50377.1/s
[progress] 8800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8800) elapsed=0.2s rate=50449.4/s
[progress] 8900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8900) elapsed=0.2s rate=50466.2/s
[progress] 9000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9000) elapsed=0.2s rate=50386.3/s
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[progress] 9200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9200) elapsed=0.2s rate=50517.8/s
[progress] 9300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9300) elapsed=0.2s rate=50591.5/s
[progress] 9400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9400) elapsed=0.2s rate=50238.5/s
[progress] 9500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9500) elapsed=0.2s rate=50329.7/s
[progress] 9600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9600) elapsed=0.2s rate=50488.5/s
[progress] 9700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9700) elapsed=0.2s rate=50654.3/s
[progress] 9800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9800) elapsed=0.2s rate=50737.3/s
[progress] 9900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9900) elapsed=0.2s rate=50797.3/s
[progress] 10000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10000) elapsed=0.2s rate=50575.3/s
[progress] 10100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10100) elapsed=0.2s rate=50679.7/s
[progress] 10200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10200) elapsed=0.2s rate=50747.9/s
[chrom] chr7 done in 0.0s
[chrom] starting chr8
[progress] 10300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10300) elapsed=0.2s rate=50866.2/s
[progress] 10400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10400) elapsed=0.2s rate=50963.1/s
[progress] 10500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10500) elapsed=0.2s rate=50737.3/s
[progress] 10600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10600) elapsed=0.2s rate=50787.1/s
[progress] 10700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10700) elapsed=0.2s rate=50834.2/s
[progress] 10800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10800) elapsed=0.2s rate=50883.1/s
[progress] 10900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10900) elapsed=0.2s rate=50810.8/s
[progress] 11000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11000) elapsed=0.2s rate=50894.0/s
[chrom] chr8 done in 0.0s
[chrom] starting chr9
[progress] 11100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11100) elapsed=0.2s rate=50952.9/s
[progress] 11200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11200) elapsed=0.2s rate=50974.9/s
[progress] 11300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11300) elapsed=0.2s rate=50976.5/s
[progress] 11400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11400) elapsed=0.2s rate=50896.8/s
[progress] 11500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11500) elapsed=0.2s rate=50912.0/s
[progress] 11600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11600) elapsed=0.2s rate=50927.8/s
[progress] 11700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11700) elapsed=0.2s rate=50959.6/s
[progress] 11800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11800) elapsed=0.2s rate=50842.3/s
[chrom] chr9 done in 0.0s
[chrom] starting chr10
[progress] 11900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11900) elapsed=0.2s rate=50877.7/s
[progress] 12000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12000) elapsed=0.2s rate=50872.6/s
[progress] 12100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12100) elapsed=0.2s rate=50907.4/s
[progress] 12200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12200) elapsed=0.2s rate=50924.8/s
[progress] 12300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12300) elapsed=0.2s rate=50750.5/s
[progress] 12400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12400) elapsed=0.2s rate=50805.0/s
[progress] 12500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12500) elapsed=0.2s rate=50843.9/s
[progress] 12600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12600) elapsed=0.2s rate=50917.7/s
[chrom] chr10 done in 0.0s
[chrom] starting chr11
[progress] 12700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12700) elapsed=0.2s rate=50808.2/s
[progress] 12800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12800) elapsed=0.3s rate=50781.7/s
[progress] 12900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12900) elapsed=0.3s rate=50862.9/s
[progress] 13000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13000) elapsed=0.3s rate=50955.8/s
[progress] 13100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13100) elapsed=0.3s rate=50996.0/s
[progress] 13200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13200) elapsed=0.3s rate=50842.7/s
[progress] 13300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13300) elapsed=0.3s rate=50838.8/s
[progress] 13400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13400) elapsed=0.3s rate=50894.4/s
[progress] 13500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13500) elapsed=0.3s rate=50889.2/s
[progress] 13600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13600) elapsed=0.3s rate=50795.4/s
[progress] 13700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13700) elapsed=0.3s rate=50860.8/s
[progress] 13800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13800) elapsed=0.3s rate=50978.8/s
[progress] 13900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13900) elapsed=0.3s rate=51024.9/s
[progress] 14000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14000) elapsed=0.3s rate=51113.2/s
[progress] 14100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14100) elapsed=0.3s rate=51165.3/s
[progress] 14200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14200) elapsed=0.3s rate=51029.0/s
[progress] 14300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14300) elapsed=0.3s rate=51084.6/s
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[progress] 14500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14500) elapsed=0.3s rate=51187.6/s
[chrom] chr11 done in 0.0s
[chrom] starting chr12
[progress] 14600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14600) elapsed=0.3s rate=51165.0/s
[progress] 14700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14700) elapsed=0.3s rate=51029.6/s
[progress] 14800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14800) elapsed=0.3s rate=51035.1/s
[progress] 14900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14900) elapsed=0.3s rate=51113.2/s
[progress] 15000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15000) elapsed=0.3s rate=51140.7/s
[progress] 15100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15100) elapsed=0.3s rate=51229.1/s
[progress] 15200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15200) elapsed=0.3s rate=51136.3/s
[progress] 15300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15300) elapsed=0.3s rate=51157.5/s
[progress] 15400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15400) elapsed=0.3s rate=51195.8/s
[progress] 15500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15500) elapsed=0.3s rate=51201.7/s
[progress] 15600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15600) elapsed=0.3s rate=51108.7/s
[progress] 15700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15700) elapsed=0.3s rate=51146.2/s
[progress] 15800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15800) elapsed=0.3s rate=51204.5/s
[chrom] chr12 done in 0.0s
[chrom] starting chr13
[progress] 15900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15900) elapsed=0.3s rate=51232.1/s
[progress] 16000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16000) elapsed=0.3s rate=51280.0/s
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[progress] 16200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16200) elapsed=0.3s rate=51271.0/s
[chrom] chr13 done in 0.0s
[chrom] starting chr14
[progress] 16300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16300) elapsed=0.3s rate=51272.4/s
[progress] 16400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16400) elapsed=0.3s rate=51301.4/s
[progress] 16500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16500) elapsed=0.3s rate=51337.3/s
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[progress] 16800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16800) elapsed=0.3s rate=51285.2/s
[progress] 16900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16900) elapsed=0.3s rate=51367.9/s
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[progress] 17100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17100) elapsed=0.3s rate=51518.5/s
[chrom] chr14 done in 0.0s
[chrom] starting chr15
[progress] 17200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17200) elapsed=0.3s rate=51584.3/s
[progress] 17300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17300) elapsed=0.3s rate=51511.3/s
[progress] 17400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17400) elapsed=0.3s rate=51532.6/s
[progress] 17500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17500) elapsed=0.3s rate=51558.2/s
[progress] 17600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17600) elapsed=0.3s rate=51591.1/s
[progress] 17700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17700) elapsed=0.3s rate=51539.9/s
[chrom] chr15 done in 0.0s
[chrom] starting chr16
[progress] 17800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17800) elapsed=0.3s rate=51551.6/s
[progress] 17900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17900) elapsed=0.3s rate=51581.4/s
[progress] 18000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18000) elapsed=0.3s rate=51632.4/s
[progress] 18100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18100) elapsed=0.4s rate=51668.2/s
[progress] 18200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18200) elapsed=0.4s rate=51625.6/s
[progress] 18300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18300) elapsed=0.4s rate=51710.0/s
[progress] 18400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18400) elapsed=0.4s rate=51796.2/s
[progress] 18500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18500) elapsed=0.4s rate=51822.2/s
[progress] 18600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18600) elapsed=0.4s rate=51870.7/s
[progress] 18700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18700) elapsed=0.4s rate=51894.9/s
[progress] 18800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18800) elapsed=0.4s rate=51796.1/s
[progress] 18900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18900) elapsed=0.4s rate=51839.5/s
[chrom] chr16 done in 0.0s
[chrom] starting chr17
[progress] 19000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19000) elapsed=0.4s rate=51870.1/s
[progress] 19100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19100) elapsed=0.4s rate=51923.3/s
[progress] 19200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19200) elapsed=0.4s rate=51973.7/s
[progress] 19300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19300) elapsed=0.4s rate=51945.0/s
[progress] 19400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19400) elapsed=0.4s rate=51937.8/s
[progress] 19500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19500) elapsed=0.4s rate=51978.7/s
[progress] 19600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19600) elapsed=0.4s rate=51966.6/s
[progress] 19700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19700) elapsed=0.4s rate=52004.0/s
[progress] 19800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19800) elapsed=0.4s rate=51995.6/s
[progress] 19900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19900) elapsed=0.4s rate=52045.9/s
[progress] 20000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20000) elapsed=0.4s rate=52109.0/s
[progress] 20100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20100) elapsed=0.4s rate=52142.2/s
[progress] 20200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20200) elapsed=0.4s rate=52190.7/s
[progress] 20300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20300) elapsed=0.4s rate=52240.5/s
[progress] 20400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20400) elapsed=0.4s rate=52173.0/s
[progress] 20500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20500) elapsed=0.4s rate=52204.9/s
[progress] 20600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20600) elapsed=0.4s rate=52225.1/s
[chrom] chr17 done in 0.0s
[chrom] starting chr18
[progress] 20700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20700) elapsed=0.4s rate=52240.8/s
[progress] 20800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20800) elapsed=0.4s rate=52266.9/s
[progress] 20900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20900) elapsed=0.4s rate=52165.2/s
[chrom] chr18 done in 0.0s
[chrom] starting chr19
[progress] 21000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21000) elapsed=0.4s rate=52178.0/s
[progress] 21100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21100) elapsed=0.4s rate=52211.4/s
[progress] 21200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21200) elapsed=0.4s rate=52257.6/s
[progress] 21300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21300) elapsed=0.4s rate=52195.7/s
[progress] 21400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21400) elapsed=0.4s rate=52214.6/s
[progress] 21500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21500) elapsed=0.4s rate=52261.3/s
[progress] 21600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21600) elapsed=0.4s rate=52302.3/s
[progress] 21700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21700) elapsed=0.4s rate=52369.7/s
[progress] 21800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21800) elapsed=0.4s rate=52423.6/s
[progress] 21900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21900) elapsed=0.4s rate=52372.1/s
[progress] 22000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22000) elapsed=0.4s rate=52402.6/s
[progress] 22100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22100) elapsed=0.4s rate=52467.9/s
[progress] 22200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22200) elapsed=0.4s rate=52518.9/s
[progress] 22300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22300) elapsed=0.4s rate=52575.8/s
[progress] 22400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22400) elapsed=0.4s rate=52630.0/s
[progress] 22500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22500) elapsed=0.4s rate=52657.9/s
[progress] 22600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22600) elapsed=0.4s rate=52602.0/s
[progress] 22700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22700) elapsed=0.4s rate=52641.5/s
[progress] 22800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22800) elapsed=0.4s rate=52665.2/s
[progress] 22900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22900) elapsed=0.4s rate=52712.2/s
[progress] 23000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23000) elapsed=0.4s rate=52763.6/s
[progress] 23100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23100) elapsed=0.4s rate=52799.4/s
[progress] 23200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23200) elapsed=0.4s rate=52759.7/s
[progress] 23300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23300) elapsed=0.4s rate=52795.2/s
[progress] 23400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23400) elapsed=0.4s rate=52852.4/s
[progress] 23500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23500) elapsed=0.4s rate=52879.3/s
[progress] 23600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23600) elapsed=0.4s rate=52924.2/s
[progress] 23700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23700) elapsed=0.4s rate=52866.8/s
[progress] 23800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23800) elapsed=0.4s rate=52927.0/s
[progress] 23900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23900) elapsed=0.5s rate=52985.1/s
[progress] 24000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24000) elapsed=0.5s rate=53045.1/s
[progress] 24100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24100) elapsed=0.5s rate=53103.7/s
[progress] 24200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24200) elapsed=0.5s rate=53132.8/s
[progress] 24300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24300) elapsed=0.5s rate=53105.8/s
[progress] 24400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24400) elapsed=0.5s rate=53021.8/s
[progress] 24500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24500) elapsed=0.5s rate=53077.4/s
[progress] 24600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24600) elapsed=0.5s rate=53133.2/s
[progress] 24700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24700) elapsed=0.5s rate=53176.9/s
[chrom] chr19 done in 0.1s
[chrom] starting chr20
[progress] 24800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24800) elapsed=0.5s rate=53192.2/s
[progress] 24900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24900) elapsed=0.5s rate=53251.8/s
[progress] 25000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25000) elapsed=0.5s rate=53227.6/s
[progress] 25100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25100) elapsed=0.5s rate=53254.5/s
[progress] 25200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25200) elapsed=0.5s rate=53286.7/s
[progress] 25300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25300) elapsed=0.5s rate=53329.0/s
[chrom] chr20 done in 0.0s
[chrom] starting chr21
[progress] 25400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25400) elapsed=0.5s rate=53376.9/s
[progress] 25500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25500) elapsed=0.5s rate=53386.9/s
[progress] 25600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25600) elapsed=0.5s rate=53356.3/s
[chrom] chr21 done in 0.0s
[chrom] starting chr22
[progress] 25700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25700) elapsed=0.5s rate=53391.6/s
[progress] 25800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25800) elapsed=0.5s rate=53428.8/s
[progress] 25900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25900) elapsed=0.5s rate=53463.9/s
[progress] 26000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26000) elapsed=0.5s rate=53480.2/s
[progress] 26100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26100) elapsed=0.5s rate=53524.3/s
[progress] 26200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26200) elapsed=0.5s rate=53472.5/s
[progress] 26300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26300) elapsed=0.5s rate=53484.2/s
[chrom] chr22 done in 0.0s
[chrom] starting chrX
[progress] 26400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26400) elapsed=0.5s rate=53515.8/s
[progress] 26500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26500) elapsed=0.5s rate=53550.2/s
[progress] 26600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26600) elapsed=0.5s rate=53578.0/s
[progress] 26700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26700) elapsed=0.5s rate=53602.8/s
[progress] 26800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26800) elapsed=0.5s rate=53591.0/s
[progress] 26900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26900) elapsed=0.5s rate=53625.8/s
[progress] 27000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27000) elapsed=0.5s rate=53660.6/s
[progress] 27100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27100) elapsed=0.5s rate=53691.1/s
[progress] 27200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27200) elapsed=0.5s rate=53735.0/s
[progress] 27300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27300) elapsed=0.5s rate=53778.6/s
[progress] 27400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27400) elapsed=0.5s rate=53799.9/s
[progress] 27500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27500) elapsed=0.5s rate=53826.6/s
[progress] 27600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27600) elapsed=0.5s rate=53852.4/s
[chrom] chrX done in 0.0s
[done] 27624 variants in 0.5s (ok=0 no_reads=0 ref_mismatch=0 other=27624)