[init] ff = 0.050
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG02622_x_HG02630_FF_5.mix.bam
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 30156 sites
[chrom] starting chr1
[progress] 100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=100) elapsed=0.0s rate=41585.4/s
[progress] 200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=200) elapsed=0.0s rate=43296.0/s
[progress] 300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=300) elapsed=0.0s rate=43274.5/s
[progress] 400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=400) elapsed=0.0s rate=43593.0/s
[progress] 500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=500) elapsed=0.0s rate=45329.1/s
[progress] 600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=600) elapsed=0.0s rate=45487.3/s
[progress] 700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=700) elapsed=0.0s rate=46827.9/s
[progress] 800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=800) elapsed=0.0s rate=48290.2/s
[progress] 900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=900) elapsed=0.0s rate=49440.4/s
[progress] 1000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1000) elapsed=0.0s rate=50072.3/s
[progress] 1100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1100) elapsed=0.0s rate=48791.1/s
[progress] 1200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1200) elapsed=0.0s rate=49281.9/s
[progress] 1300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1300) elapsed=0.0s rate=49444.1/s
[progress] 1400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1400) elapsed=0.0s rate=49541.7/s
[progress] 1500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1500) elapsed=0.0s rate=48903.3/s
[progress] 1600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1600) elapsed=0.0s rate=49773.3/s
[progress] 1700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1700) elapsed=0.0s rate=50366.4/s
[progress] 1800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1800) elapsed=0.0s rate=51109.9/s
[progress] 1900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1900) elapsed=0.0s rate=51653.0/s
[progress] 2000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2000) elapsed=0.0s rate=52243.3/s
[progress] 2100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2100) elapsed=0.0s rate=51447.6/s
[progress] 2200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2200) elapsed=0.0s rate=51576.9/s
[progress] 2300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2300) elapsed=0.0s rate=51577.5/s
[progress] 2400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2400) elapsed=0.0s rate=51867.4/s
[progress] 2500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2500) elapsed=0.0s rate=51107.2/s
[progress] 2600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2600) elapsed=0.1s rate=51333.0/s
[progress] 2700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2700) elapsed=0.1s rate=51694.3/s
[progress] 2800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2800) elapsed=0.1s rate=51786.1/s
[progress] 2900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2900) elapsed=0.1s rate=51893.3/s
[chrom] chr1 done in 0.1s
[chrom] starting chr2
[progress] 3000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3000) elapsed=0.1s rate=51457.3/s
[progress] 3100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3100) elapsed=0.1s rate=51612.6/s
[progress] 3200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3200) elapsed=0.1s rate=51684.0/s
[progress] 3300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3300) elapsed=0.1s rate=51879.2/s
[progress] 3400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3400) elapsed=0.1s rate=52208.4/s
[progress] 3500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3500) elapsed=0.1s rate=51977.7/s
[progress] 3600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3600) elapsed=0.1s rate=52077.1/s
[progress] 3700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3700) elapsed=0.1s rate=52154.6/s
[progress] 3800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3800) elapsed=0.1s rate=52164.9/s
[progress] 3900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3900) elapsed=0.1s rate=51536.3/s
[progress] 4000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4000) elapsed=0.1s rate=51673.2/s
[progress] 4100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4100) elapsed=0.1s rate=51745.4/s
[progress] 4200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4200) elapsed=0.1s rate=51645.5/s
[progress] 4300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4300) elapsed=0.1s rate=51415.1/s
[progress] 4400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4400) elapsed=0.1s rate=51466.3/s
[chrom] chr2 done in 0.0s
[chrom] starting chr3
[progress] 4500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4500) elapsed=0.1s rate=51682.1/s
[progress] 4600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4600) elapsed=0.1s rate=51792.9/s
[progress] 4700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4700) elapsed=0.1s rate=51949.2/s
[progress] 4800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4800) elapsed=0.1s rate=51790.5/s
[progress] 4900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4900) elapsed=0.1s rate=51970.7/s
[progress] 5000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5000) elapsed=0.1s rate=52125.9/s
[progress] 5100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5100) elapsed=0.1s rate=52194.8/s
[progress] 5200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5200) elapsed=0.1s rate=52317.0/s
[progress] 5300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5300) elapsed=0.1s rate=51790.3/s
[progress] 5400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5400) elapsed=0.1s rate=51830.9/s
[progress] 5500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5500) elapsed=0.1s rate=51828.4/s
[progress] 5600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5600) elapsed=0.1s rate=51743.3/s
[progress] 5700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5700) elapsed=0.1s rate=51272.9/s
[progress] 5800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5800) elapsed=0.1s rate=51264.7/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=51362.1/s
[progress] 6000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6000) elapsed=0.1s rate=51569.3/s
[progress] 6100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6100) elapsed=0.1s rate=51702.2/s
[progress] 6200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6200) elapsed=0.1s rate=51409.3/s
[progress] 6300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6300) elapsed=0.1s rate=51512.3/s
[progress] 6400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6400) elapsed=0.1s rate=51510.5/s
[progress] 6500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6500) elapsed=0.1s rate=51583.3/s
[progress] 6600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6600) elapsed=0.1s rate=51737.3/s
[progress] 6700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6700) elapsed=0.1s rate=51311.0/s
[progress] 6800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6800) elapsed=0.1s rate=51418.1/s
[progress] 6900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6900) elapsed=0.1s rate=51483.8/s
[chrom] chr4 done in 0.0s
[chrom] starting chr5
[progress] 7000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7000) elapsed=0.1s rate=51412.6/s
[progress] 7100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7100) elapsed=0.1s rate=51210.3/s
[progress] 7200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7200) elapsed=0.1s rate=51089.7/s
[progress] 7300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7300) elapsed=0.1s rate=51074.5/s
[progress] 7400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7400) elapsed=0.1s rate=51146.6/s
[progress] 7500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7500) elapsed=0.1s rate=50895.5/s
[progress] 7600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7600) elapsed=0.1s rate=51005.1/s
[progress] 7700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7700) elapsed=0.2s rate=51030.3/s
[progress] 7800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7800) elapsed=0.2s rate=51162.8/s
[progress] 7900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7900) elapsed=0.2s rate=51286.8/s
[chrom] chr5 done in 0.0s
[chrom] starting chr6
[progress] 8000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8000) elapsed=0.2s rate=51408.2/s
[progress] 8100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8100) elapsed=0.2s rate=51306.8/s
[progress] 8200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8200) elapsed=0.2s rate=51338.4/s
[progress] 8300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8300) elapsed=0.2s rate=51460.4/s
[progress] 8400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8400) elapsed=0.2s rate=51635.1/s
[progress] 8500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8500) elapsed=0.2s rate=51697.0/s
[progress] 8600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8600) elapsed=0.2s rate=51812.9/s
[progress] 8700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8700) elapsed=0.2s rate=51550.3/s
[progress] 8800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8800) elapsed=0.2s rate=51585.9/s
[progress] 8900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8900) elapsed=0.2s rate=51643.8/s
[progress] 9000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9000) elapsed=0.2s rate=51647.2/s
[progress] 9100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9100) elapsed=0.2s rate=51474.1/s
[progress] 9200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9200) elapsed=0.2s rate=51509.5/s
[progress] 9300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9300) elapsed=0.2s rate=51503.4/s
[progress] 9400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9400) elapsed=0.2s rate=51592.5/s
[chrom] chr6 done in 0.0s
[chrom] starting chr7
[progress] 9500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9500) elapsed=0.2s rate=51402.8/s
[progress] 9600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9600) elapsed=0.2s rate=51493.6/s
[progress] 9700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9700) elapsed=0.2s rate=51532.8/s
[progress] 9800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9800) elapsed=0.2s rate=51597.5/s
[progress] 9900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9900) elapsed=0.2s rate=51675.4/s
[progress] 10000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10000) elapsed=0.2s rate=51549.6/s
[progress] 10100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10100) elapsed=0.2s rate=51591.5/s
[progress] 10200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10200) elapsed=0.2s rate=51648.3/s
[progress] 10300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10300) elapsed=0.2s rate=51669.6/s
[progress] 10400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10400) elapsed=0.2s rate=51366.6/s
[progress] 10500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10500) elapsed=0.2s rate=51415.1/s
[progress] 10600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10600) elapsed=0.2s rate=51493.8/s
[progress] 10700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10700) elapsed=0.2s rate=51581.2/s
[progress] 10800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10800) elapsed=0.2s rate=51633.5/s
[progress] 10900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10900) elapsed=0.2s rate=51464.8/s
[progress] 11000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11000) elapsed=0.2s rate=51524.3/s
[progress] 11100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11100) elapsed=0.2s rate=51617.4/s
[chrom] chr7 done in 0.0s
[chrom] starting chr8
[progress] 11200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11200) elapsed=0.2s rate=51681.8/s
[progress] 11300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11300) elapsed=0.2s rate=51713.3/s
[progress] 11400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11400) elapsed=0.2s rate=51600.5/s
[progress] 11500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11500) elapsed=0.2s rate=51646.7/s
[progress] 11600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11600) elapsed=0.2s rate=51603.3/s
[progress] 11700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11700) elapsed=0.2s rate=51645.6/s
[progress] 11800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11800) elapsed=0.2s rate=51548.4/s
[progress] 11900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11900) elapsed=0.2s rate=51628.8/s
[chrom] chr8 done in 0.0s
[chrom] starting chr9
[progress] 12000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12000) elapsed=0.2s rate=51718.5/s
[progress] 12100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12100) elapsed=0.2s rate=51748.6/s
[progress] 12200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12200) elapsed=0.2s rate=51817.0/s
[progress] 12300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12300) elapsed=0.2s rate=51651.5/s
[progress] 12400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12400) elapsed=0.2s rate=51706.0/s
[progress] 12500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12500) elapsed=0.2s rate=51702.9/s
[progress] 12600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12600) elapsed=0.2s rate=51741.5/s
[progress] 12700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12700) elapsed=0.2s rate=51793.1/s
[progress] 12800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12800) elapsed=0.2s rate=51639.1/s
[progress] 12900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12900) elapsed=0.2s rate=51708.0/s
[chrom] chr9 done in 0.0s
[chrom] starting chr10
[progress] 13000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13000) elapsed=0.3s rate=51704.5/s
[progress] 13100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13100) elapsed=0.3s rate=51744.6/s
[progress] 13200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13200) elapsed=0.3s rate=51636.2/s
[progress] 13300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13300) elapsed=0.3s rate=51681.4/s
[progress] 13400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13400) elapsed=0.3s rate=51764.1/s
[progress] 13500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13500) elapsed=0.3s rate=51792.0/s
[progress] 13600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13600) elapsed=0.3s rate=51875.9/s
[progress] 13700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13700) elapsed=0.3s rate=51764.7/s
[progress] 13800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13800) elapsed=0.3s rate=51856.9/s
[chrom] chr10 done in 0.0s
[chrom] starting chr11
[progress] 13900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13900) elapsed=0.3s rate=51897.2/s
[progress] 14000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14000) elapsed=0.3s rate=51897.8/s
[progress] 14100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14100) elapsed=0.3s rate=51967.5/s
[progress] 14200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14200) elapsed=0.3s rate=52048.2/s
[progress] 14300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14300) elapsed=0.3s rate=51956.4/s
[progress] 14400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14400) elapsed=0.3s rate=51983.9/s
[progress] 14500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14500) elapsed=0.3s rate=52001.3/s
[progress] 14600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14600) elapsed=0.3s rate=51934.6/s
[progress] 14700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14700) elapsed=0.3s rate=51984.9/s
[progress] 14800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14800) elapsed=0.3s rate=51760.1/s
[progress] 14900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14900) elapsed=0.3s rate=51795.2/s
[progress] 15000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15000) elapsed=0.3s rate=51869.2/s
[progress] 15100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15100) elapsed=0.3s rate=51891.0/s
[progress] 15200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15200) elapsed=0.3s rate=51923.3/s
[progress] 15300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15300) elapsed=0.3s rate=51831.4/s
[progress] 15400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15400) elapsed=0.3s rate=51867.2/s
[progress] 15500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15500) elapsed=0.3s rate=51908.5/s
[progress] 15600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15600) elapsed=0.3s rate=51932.6/s
[progress] 15700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15700) elapsed=0.3s rate=51970.0/s
[progress] 15800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15800) elapsed=0.3s rate=51876.1/s
[progress] 15900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15900) elapsed=0.3s rate=51873.6/s
[chrom] chr11 done in 0.0s
[chrom] starting chr12
[progress] 16000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16000) elapsed=0.3s rate=51901.1/s
[progress] 16100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16100) elapsed=0.3s rate=51913.3/s
[progress] 16200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16200) elapsed=0.3s rate=51751.1/s
[progress] 16300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16300) elapsed=0.3s rate=51825.9/s
[progress] 16400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16400) elapsed=0.3s rate=51871.9/s
[progress] 16500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16500) elapsed=0.3s rate=51921.0/s
[progress] 16600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16600) elapsed=0.3s rate=51981.3/s
[progress] 16700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16700) elapsed=0.3s rate=52036.3/s
[progress] 16800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16800) elapsed=0.3s rate=51954.3/s
[progress] 16900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16900) elapsed=0.3s rate=51995.6/s
[progress] 17000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17000) elapsed=0.3s rate=52010.8/s
[progress] 17100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17100) elapsed=0.3s rate=52041.2/s
[progress] 17200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17200) elapsed=0.3s rate=52054.7/s
[progress] 17300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17300) elapsed=0.3s rate=51962.8/s
[chrom] chr12 done in 0.0s
[chrom] starting chr13
[progress] 17400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17400) elapsed=0.3s rate=51988.9/s
[progress] 17500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17500) elapsed=0.3s rate=52015.5/s
[progress] 17600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17600) elapsed=0.3s rate=52058.8/s
[progress] 17700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17700) elapsed=0.3s rate=51929.9/s
[chrom] chr13 done in 0.0s
[chrom] starting chr14
[progress] 17800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17800) elapsed=0.3s rate=51947.0/s
[progress] 17900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17900) elapsed=0.3s rate=51976.2/s
[progress] 18000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18000) elapsed=0.3s rate=52014.3/s
[progress] 18100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18100) elapsed=0.3s rate=52043.8/s
[progress] 18200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18200) elapsed=0.4s rate=51974.3/s
[progress] 18300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18300) elapsed=0.4s rate=52001.2/s
[progress] 18400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18400) elapsed=0.4s rate=52067.4/s
[progress] 18500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18500) elapsed=0.4s rate=52144.4/s
[progress] 18600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18600) elapsed=0.4s rate=52226.8/s
[chrom] chr14 done in 0.0s
[chrom] starting chr15
[progress] 18700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18700) elapsed=0.4s rate=52272.4/s
[progress] 18800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18800) elapsed=0.4s rate=52181.3/s
[progress] 18900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18900) elapsed=0.4s rate=52184.5/s
[progress] 19000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19000) elapsed=0.4s rate=52203.5/s
[progress] 19100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19100) elapsed=0.4s rate=52212.7/s
[progress] 19200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19200) elapsed=0.4s rate=52115.2/s
[chrom] chr15 done in 0.0s
[chrom] starting chr16
[progress] 19300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19300) elapsed=0.4s rate=52133.5/s
[progress] 19400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19400) elapsed=0.4s rate=52143.2/s
[progress] 19500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19500) elapsed=0.4s rate=52187.1/s
[progress] 19600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19600) elapsed=0.4s rate=52212.3/s
[progress] 19700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19700) elapsed=0.4s rate=52140.4/s
[progress] 19800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19800) elapsed=0.4s rate=52194.3/s
[progress] 19900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19900) elapsed=0.4s rate=52244.8/s
[progress] 20000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20000) elapsed=0.4s rate=52309.3/s
[progress] 20100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20100) elapsed=0.4s rate=52355.0/s
[progress] 20200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20200) elapsed=0.4s rate=52281.2/s
[progress] 20300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20300) elapsed=0.4s rate=52316.7/s
[progress] 20400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20400) elapsed=0.4s rate=52324.5/s
[progress] 20500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20500) elapsed=0.4s rate=52293.1/s
[progress] 20600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20600) elapsed=0.4s rate=52318.7/s
[chrom] chr16 done in 0.0s
[chrom] starting chr17
[progress] 20700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20700) elapsed=0.4s rate=52250.8/s
[progress] 20800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20800) elapsed=0.4s rate=52272.0/s
[progress] 20900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20900) elapsed=0.4s rate=52307.5/s
[progress] 21000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21000) elapsed=0.4s rate=52341.8/s
[progress] 21100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21100) elapsed=0.4s rate=52349.3/s
[progress] 21200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21200) elapsed=0.4s rate=52393.0/s
[progress] 21300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21300) elapsed=0.4s rate=52316.6/s
[progress] 21400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21400) elapsed=0.4s rate=52331.5/s
[progress] 21500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21500) elapsed=0.4s rate=52353.4/s
[progress] 21600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21600) elapsed=0.4s rate=52409.7/s
[progress] 21700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21700) elapsed=0.4s rate=52445.2/s
[progress] 21800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21800) elapsed=0.4s rate=52372.2/s
[progress] 21900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21900) elapsed=0.4s rate=52408.3/s
[progress] 22000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22000) elapsed=0.4s rate=52427.2/s
[progress] 22100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22100) elapsed=0.4s rate=52382.4/s
[progress] 22200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22200) elapsed=0.4s rate=52384.2/s
[progress] 22300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22300) elapsed=0.4s rate=52280.1/s
[progress] 22400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22400) elapsed=0.4s rate=52277.5/s
[progress] 22500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22500) elapsed=0.4s rate=52280.0/s
[chrom] chr17 done in 0.0s
[chrom] starting chr18
[progress] 22600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22600) elapsed=0.4s rate=52215.5/s
[progress] 22700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22700) elapsed=0.4s rate=51600.6/s
[progress] 22800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22800) elapsed=0.4s rate=51487.9/s
[chrom] chr18 done in 0.0s
[chrom] starting chr19
[progress] 22900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22900) elapsed=0.4s rate=51503.8/s
[progress] 23000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23000) elapsed=0.4s rate=51557.1/s
[progress] 23100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23100) elapsed=0.4s rate=51585.8/s
[progress] 23200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23200) elapsed=0.4s rate=51579.8/s
[progress] 23300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23300) elapsed=0.5s rate=51514.8/s
[progress] 23400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23400) elapsed=0.5s rate=51558.9/s
[progress] 23500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23500) elapsed=0.5s rate=51588.0/s
[progress] 23600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23600) elapsed=0.5s rate=51650.4/s
[progress] 23700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23700) elapsed=0.5s rate=51704.3/s
[progress] 23800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23800) elapsed=0.5s rate=51737.1/s
[progress] 23900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23900) elapsed=0.5s rate=51676.8/s
[progress] 24000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24000) elapsed=0.5s rate=51701.2/s
[progress] 24100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24100) elapsed=0.5s rate=51760.8/s
[progress] 24200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24200) elapsed=0.5s rate=51812.4/s
[progress] 24300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24300) elapsed=0.5s rate=51853.5/s
[progress] 24400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24400) elapsed=0.5s rate=51895.7/s
[progress] 24500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24500) elapsed=0.5s rate=51959.6/s
[progress] 24600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24600) elapsed=0.5s rate=51931.5/s
[progress] 24700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24700) elapsed=0.5s rate=51986.5/s
[progress] 24800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24800) elapsed=0.5s rate=52023.7/s
[progress] 24900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24900) elapsed=0.5s rate=52065.5/s
[progress] 25000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25000) elapsed=0.5s rate=52076.7/s
[progress] 25100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25100) elapsed=0.5s rate=52126.1/s
[progress] 25200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25200) elapsed=0.5s rate=52069.1/s
[progress] 25300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25300) elapsed=0.5s rate=52100.7/s
[progress] 25400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25400) elapsed=0.5s rate=52134.4/s
[progress] 25500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25500) elapsed=0.5s rate=52183.4/s
[progress] 25600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25600) elapsed=0.5s rate=52210.3/s
[progress] 25700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25700) elapsed=0.5s rate=52238.8/s
[progress] 25800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25800) elapsed=0.5s rate=52180.2/s
[progress] 25900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25900) elapsed=0.5s rate=52212.0/s
[progress] 26000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26000) elapsed=0.5s rate=52235.8/s
[progress] 26100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26100) elapsed=0.5s rate=52284.8/s
[progress] 26200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26200) elapsed=0.5s rate=52317.3/s
[progress] 26300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26300) elapsed=0.5s rate=52301.8/s
[progress] 26400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26400) elapsed=0.5s rate=52189.0/s
[progress] 26500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26500) elapsed=0.5s rate=52157.1/s
[progress] 26600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26600) elapsed=0.5s rate=52171.2/s
[progress] 26700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26700) elapsed=0.5s rate=52215.1/s
[progress] 26800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26800) elapsed=0.5s rate=52265.8/s
[progress] 26900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26900) elapsed=0.5s rate=52307.0/s
[progress] 27000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27000) elapsed=0.5s rate=52358.0/s
[chrom] chr19 done in 0.1s
[chrom] starting chr20
[progress] 27100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27100) elapsed=0.5s rate=52268.0/s
[progress] 27200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27200) elapsed=0.5s rate=52262.9/s
[progress] 27300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27300) elapsed=0.5s rate=52296.4/s
[progress] 27400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27400) elapsed=0.5s rate=52326.0/s
[progress] 27500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27500) elapsed=0.5s rate=52335.5/s
[progress] 27600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27600) elapsed=0.5s rate=52262.7/s
[progress] 27700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27700) elapsed=0.5s rate=52267.9/s
[chrom] chr20 done in 0.0s
[chrom] starting chr21
[progress] 27800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27800) elapsed=0.5s rate=52283.7/s
[progress] 27900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27900) elapsed=0.5s rate=52325.3/s
[progress] 28000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28000) elapsed=0.5s rate=52349.7/s
[chrom] chr21 done in 0.0s
[chrom] starting chr22
[progress] 28100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28100) elapsed=0.5s rate=52334.7/s
[progress] 28200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28200) elapsed=0.5s rate=52250.1/s
[progress] 28300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28300) elapsed=0.5s rate=52248.6/s
[progress] 28400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28400) elapsed=0.5s rate=52260.0/s
[progress] 28500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28500) elapsed=0.5s rate=52272.9/s
[progress] 28600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28600) elapsed=0.5s rate=52312.4/s
[progress] 28700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28700) elapsed=0.5s rate=52250.1/s
[chrom] chr22 done in 0.0s
[chrom] starting chrX
[progress] 28800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28800) elapsed=0.6s rate=52271.6/s
[progress] 28900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28900) elapsed=0.6s rate=52291.2/s
[progress] 29000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29000) elapsed=0.6s rate=52330.1/s
[progress] 29100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29100) elapsed=0.6s rate=52374.0/s
[progress] 29200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29200) elapsed=0.6s rate=52389.5/s
[progress] 29300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29300) elapsed=0.6s rate=52389.8/s
[progress] 29400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29400) elapsed=0.6s rate=52418.0/s
[progress] 29500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29500) elapsed=0.6s rate=52444.8/s
[progress] 29600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29600) elapsed=0.6s rate=52460.9/s
[progress] 29700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29700) elapsed=0.6s rate=52485.9/s
[progress] 29800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29800) elapsed=0.6s rate=52515.5/s
[progress] 29900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29900) elapsed=0.6s rate=52548.9/s
[progress] 30000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30000) elapsed=0.6s rate=52549.6/s
[progress] 30100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30100) elapsed=0.6s rate=52573.1/s
[chrom] chrX done in 0.0s
[done] 30158 variants in 0.6s (ok=0 no_reads=0 ref_mismatch=0 other=30158)