Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/bc38c5bfb057f9c181ba232c9897ab/.command.sh
  Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/7ca459b5c4f4700bf7b3e2d3de4748/HG03540_x_HG03579_FF_10.mix.bam
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/targets/HG03540_x_HG03579_FF_10.targets.tsv
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/vcfs/HG03540_x_HG03579_FF_10.vcf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/bc38c5bfb057f9c181ba232c9897ab/.command.run
==> STAGING COMPLETE (7 inputs)

[init] ff = 0.100
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG03540_x_HG03579_FF_10.mix.bam
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 37524 sites
[chrom] starting chr1
[progress] 100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=100) elapsed=0.0s rate=41519.5/s
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[progress] 3200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3200) elapsed=0.1s rate=59756.7/s
[progress] 3300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3300) elapsed=0.1s rate=59907.7/s
[progress] 3400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3400) elapsed=0.1s rate=60107.0/s
[progress] 3500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3500) elapsed=0.1s rate=60221.5/s
[progress] 3600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3600) elapsed=0.1s rate=60221.6/s
[progress] 3700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3700) elapsed=0.1s rate=60304.2/s
[progress] 3800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3800) elapsed=0.1s rate=59819.2/s
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[progress] 4000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4000) elapsed=0.1s rate=60034.2/s
[chrom] chr1 done in 0.1s
[chrom] starting chr2
[progress] 4100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4100) elapsed=0.1s rate=60081.5/s
[progress] 4200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4200) elapsed=0.1s rate=60242.8/s
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[progress] 5700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5700) elapsed=0.1s rate=60758.4/s
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[progress] 6300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6300) elapsed=0.1s rate=60832.5/s
[chrom] chr2 done in 0.0s
[chrom] starting chr3
[progress] 6400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6400) elapsed=0.1s rate=60842.3/s
[progress] 6500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6500) elapsed=0.1s rate=60998.0/s
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[progress] 6900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6900) elapsed=0.1s rate=61078.0/s
[progress] 7000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7000) elapsed=0.1s rate=61233.3/s
[progress] 7100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7100) elapsed=0.1s rate=61345.9/s
[progress] 7200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7200) elapsed=0.1s rate=61478.3/s
[progress] 7300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7300) elapsed=0.1s rate=61557.3/s
[progress] 7400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7400) elapsed=0.1s rate=61079.4/s
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[progress] 8400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8400) elapsed=0.1s rate=61286.3/s
[chrom] chr3 done in 0.0s
[chrom] starting chr4
[progress] 8500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8500) elapsed=0.1s rate=61363.9/s
[progress] 8600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8600) elapsed=0.1s rate=61415.1/s
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[progress] 9300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9300) elapsed=0.2s rate=61603.0/s
[progress] 9400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9400) elapsed=0.2s rate=61330.8/s
[progress] 9500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9500) elapsed=0.2s rate=61431.3/s
[progress] 9600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9600) elapsed=0.2s rate=61482.2/s
[progress] 9700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9700) elapsed=0.2s rate=61541.4/s
[chrom] chr4 done in 0.0s
[chrom] starting chr5
[progress] 9800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9800) elapsed=0.2s rate=61567.6/s
[progress] 9900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9900) elapsed=0.2s rate=61665.9/s
[progress] 10000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10000) elapsed=0.2s rate=61668.1/s
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[progress] 10500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10500) elapsed=0.2s rate=61700.1/s
[progress] 10600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10600) elapsed=0.2s rate=61731.3/s
[progress] 10700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10700) elapsed=0.2s rate=61786.4/s
[progress] 10800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10800) elapsed=0.2s rate=61674.5/s
[progress] 10900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10900) elapsed=0.2s rate=61726.5/s
[progress] 11000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11000) elapsed=0.2s rate=61800.9/s
[progress] 11100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11100) elapsed=0.2s rate=61872.4/s
[progress] 11200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11200) elapsed=0.2s rate=61957.4/s
[progress] 11300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11300) elapsed=0.2s rate=62002.0/s
[chrom] chr5 done in 0.0s
[chrom] starting chr6
[progress] 11400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11400) elapsed=0.2s rate=62049.5/s
[progress] 11500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11500) elapsed=0.2s rate=62102.1/s
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[progress] 12000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12000) elapsed=0.2s rate=61849.1/s
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[progress] 12300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12300) elapsed=0.2s rate=61751.2/s
[progress] 12400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12400) elapsed=0.2s rate=61812.6/s
[progress] 12500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12500) elapsed=0.2s rate=61833.4/s
[progress] 12600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12600) elapsed=0.2s rate=61846.1/s
[progress] 12700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12700) elapsed=0.2s rate=61914.9/s
[progress] 12800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12800) elapsed=0.2s rate=61947.5/s
[progress] 12900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12900) elapsed=0.2s rate=61803.5/s
[progress] 13000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13000) elapsed=0.2s rate=61856.1/s
[progress] 13100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13100) elapsed=0.2s rate=61860.8/s
[progress] 13200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13200) elapsed=0.2s rate=61868.3/s
[chrom] chr6 done in 0.0s
[chrom] starting chr7
[progress] 13300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13300) elapsed=0.2s rate=61919.1/s
[progress] 13400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13400) elapsed=0.2s rate=61946.1/s
[progress] 13500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13500) elapsed=0.2s rate=61998.2/s
[progress] 13600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13600) elapsed=0.2s rate=61815.6/s
[progress] 13700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13700) elapsed=0.2s rate=61828.7/s
[progress] 13800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13800) elapsed=0.2s rate=61829.3/s
[progress] 13900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13900) elapsed=0.2s rate=61861.0/s
[progress] 14000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14000) elapsed=0.2s rate=61893.9/s
[progress] 14100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14100) elapsed=0.2s rate=61932.9/s
[progress] 14200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14200) elapsed=0.2s rate=61940.0/s
[progress] 14300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14300) elapsed=0.2s rate=61477.4/s
[progress] 14400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14400) elapsed=0.2s rate=61511.8/s
[progress] 14500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14500) elapsed=0.2s rate=61507.5/s
[progress] 14600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14600) elapsed=0.2s rate=61531.0/s
[progress] 14700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14700) elapsed=0.2s rate=61436.0/s
[progress] 14800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14800) elapsed=0.2s rate=61480.1/s
[progress] 14900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14900) elapsed=0.2s rate=61471.4/s
[progress] 15000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15000) elapsed=0.2s rate=61471.0/s
[progress] 15100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15100) elapsed=0.2s rate=61519.7/s
[chrom] chr7 done in 0.0s
[chrom] starting chr8
[progress] 15200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15200) elapsed=0.2s rate=61533.5/s
[progress] 15300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15300) elapsed=0.2s rate=61473.8/s
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[progress] 15500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15500) elapsed=0.3s rate=61134.8/s
[progress] 15600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15600) elapsed=0.3s rate=61200.9/s
[progress] 15700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15700) elapsed=0.3s rate=61174.9/s
[progress] 15800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15800) elapsed=0.3s rate=61177.0/s
[progress] 15900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15900) elapsed=0.3s rate=61169.2/s
[progress] 16000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16000) elapsed=0.3s rate=61020.5/s
[progress] 16100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16100) elapsed=0.3s rate=60921.3/s
[progress] 16200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16200) elapsed=0.3s rate=60949.1/s
[chrom] chr8 done in 0.0s
[chrom] starting chr9
[progress] 16300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16300) elapsed=0.3s rate=60970.7/s
[progress] 16400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16400) elapsed=0.3s rate=60977.4/s
[progress] 16500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16500) elapsed=0.3s rate=61015.7/s
[progress] 16600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16600) elapsed=0.3s rate=60996.1/s
[progress] 16700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16700) elapsed=0.3s rate=61034.9/s
[progress] 16800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16800) elapsed=0.3s rate=60949.2/s
[progress] 16900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16900) elapsed=0.3s rate=60981.0/s
[progress] 17000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17000) elapsed=0.3s rate=61022.1/s
[progress] 17100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17100) elapsed=0.3s rate=61045.9/s
[progress] 17200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17200) elapsed=0.3s rate=61064.3/s
[progress] 17300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17300) elapsed=0.3s rate=61105.3/s
[progress] 17400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17400) elapsed=0.3s rate=61136.8/s
[progress] 17500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17500) elapsed=0.3s rate=60998.8/s
[progress] 17600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17600) elapsed=0.3s rate=61041.7/s
[chrom] chr9 done in 0.0s
[chrom] starting chr10
[progress] 17700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17700) elapsed=0.3s rate=61062.6/s
[progress] 17800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17800) elapsed=0.3s rate=61096.8/s
[progress] 17900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17900) elapsed=0.3s rate=61125.5/s
[progress] 18000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18000) elapsed=0.3s rate=61143.3/s
[progress] 18100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18100) elapsed=0.3s rate=61183.3/s
[progress] 18200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18200) elapsed=0.3s rate=61039.3/s
[progress] 18300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18300) elapsed=0.3s rate=61067.1/s
[progress] 18400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18400) elapsed=0.3s rate=61104.0/s
[progress] 18500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18500) elapsed=0.3s rate=61133.2/s
[progress] 18600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18600) elapsed=0.3s rate=61194.0/s
[progress] 18700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18700) elapsed=0.3s rate=61240.2/s
[progress] 18800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18800) elapsed=0.3s rate=61290.0/s
[progress] 18900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18900) elapsed=0.3s rate=61322.5/s
[progress] 19000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19000) elapsed=0.3s rate=61212.1/s
[chrom] chr10 done in 0.0s
[chrom] starting chr11
[progress] 19100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19100) elapsed=0.3s rate=61222.2/s
[progress] 19200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19200) elapsed=0.3s rate=61208.9/s
[progress] 19300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19300) elapsed=0.3s rate=61189.2/s
[progress] 19400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19400) elapsed=0.3s rate=61233.6/s
[progress] 19500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19500) elapsed=0.3s rate=61279.3/s
[progress] 19600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19600) elapsed=0.3s rate=61138.5/s
[progress] 19700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19700) elapsed=0.3s rate=61173.0/s
[progress] 19800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19800) elapsed=0.3s rate=61202.4/s
[progress] 19900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19900) elapsed=0.3s rate=61241.1/s
[progress] 20000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20000) elapsed=0.3s rate=61274.8/s
[progress] 20100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20100) elapsed=0.3s rate=61317.5/s
[progress] 20200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20200) elapsed=0.3s rate=61306.2/s
[progress] 20300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20300) elapsed=0.3s rate=61202.5/s
[progress] 20400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20400) elapsed=0.3s rate=61204.5/s
[progress] 20500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20500) elapsed=0.3s rate=61224.7/s
[progress] 20600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20600) elapsed=0.3s rate=61280.5/s
[progress] 20700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20700) elapsed=0.3s rate=61329.4/s
[progress] 20800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20800) elapsed=0.3s rate=61385.9/s
[progress] 20900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20900) elapsed=0.3s rate=61416.1/s
[progress] 21000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21000) elapsed=0.3s rate=61409.5/s
[progress] 21100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21100) elapsed=0.3s rate=61286.4/s
[progress] 21200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21200) elapsed=0.3s rate=61303.1/s
[progress] 21300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21300) elapsed=0.3s rate=61316.5/s
[progress] 21400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21400) elapsed=0.3s rate=61352.8/s
[progress] 21500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21500) elapsed=0.4s rate=61393.4/s
[progress] 21600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21600) elapsed=0.4s rate=61380.7/s
[chrom] chr11 done in 0.0s
[chrom] starting chr12
[progress] 21700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21700) elapsed=0.4s rate=61304.0/s
[progress] 21800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21800) elapsed=0.4s rate=61316.8/s
[progress] 21900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21900) elapsed=0.4s rate=61294.2/s
[progress] 22000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22000) elapsed=0.4s rate=61320.9/s
[progress] 22100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22100) elapsed=0.4s rate=61343.4/s
[progress] 22200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22200) elapsed=0.4s rate=61381.4/s
[progress] 22300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22300) elapsed=0.4s rate=61401.0/s
[progress] 22400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22400) elapsed=0.4s rate=61361.4/s
[progress] 22500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22500) elapsed=0.4s rate=61399.8/s
[progress] 22600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22600) elapsed=0.4s rate=61416.5/s
[progress] 22700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22700) elapsed=0.4s rate=61465.3/s
[progress] 22800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22800) elapsed=0.4s rate=61482.1/s
[progress] 22900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22900) elapsed=0.4s rate=61495.3/s
[progress] 23000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23000) elapsed=0.4s rate=61538.7/s
[progress] 23100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23100) elapsed=0.4s rate=61442.5/s
[progress] 23200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23200) elapsed=0.4s rate=61474.7/s
[progress] 23300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23300) elapsed=0.4s rate=61504.2/s
[chrom] chr12 done in 0.0s
[chrom] starting chr13
[progress] 23400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23400) elapsed=0.4s rate=61513.2/s
[progress] 23500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23500) elapsed=0.4s rate=61517.4/s
[progress] 23600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23600) elapsed=0.4s rate=61536.4/s
[progress] 23700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23700) elapsed=0.4s rate=61514.2/s
[chrom] chr13 done in 0.0s
[chrom] starting chr14
[progress] 23800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23800) elapsed=0.4s rate=61431.9/s
[progress] 23900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23900) elapsed=0.4s rate=61460.3/s
[progress] 24000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24000) elapsed=0.4s rate=61492.4/s
[progress] 24100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24100) elapsed=0.4s rate=61511.3/s
[progress] 24200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24200) elapsed=0.4s rate=61523.8/s
[progress] 24300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24300) elapsed=0.4s rate=61569.3/s
[progress] 24400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24400) elapsed=0.4s rate=61604.8/s
[progress] 24500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24500) elapsed=0.4s rate=61545.6/s
[progress] 24600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24600) elapsed=0.4s rate=61579.6/s
[progress] 24700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24700) elapsed=0.4s rate=61606.2/s
[chrom] chr14 done in 0.0s
[chrom] starting chr15
[progress] 24800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24800) elapsed=0.4s rate=61630.7/s
[progress] 24900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24900) elapsed=0.4s rate=61635.2/s
[progress] 25000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25000) elapsed=0.4s rate=61595.0/s
[progress] 25100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25100) elapsed=0.4s rate=61387.8/s
[progress] 25200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25200) elapsed=0.4s rate=61397.1/s
[progress] 25300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25300) elapsed=0.4s rate=61396.1/s
[progress] 25400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25400) elapsed=0.4s rate=61419.9/s
[progress] 25500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25500) elapsed=0.4s rate=61429.3/s
[progress] 25600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25600) elapsed=0.4s rate=61441.5/s
[chrom] chr15 done in 0.0s
[chrom] starting chr16
[progress] 25700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25700) elapsed=0.4s rate=61473.9/s
[progress] 25800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25800) elapsed=0.4s rate=61392.7/s
[progress] 25900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25900) elapsed=0.4s rate=61417.9/s
[progress] 26000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26000) elapsed=0.4s rate=61445.3/s
[progress] 26100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26100) elapsed=0.4s rate=61471.6/s
[progress] 26200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26200) elapsed=0.4s rate=61496.1/s
[progress] 26300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26300) elapsed=0.4s rate=61522.7/s
[progress] 26400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26400) elapsed=0.4s rate=61564.3/s
[progress] 26500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26500) elapsed=0.4s rate=61610.1/s
[progress] 26600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26600) elapsed=0.4s rate=61544.6/s
[progress] 26700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26700) elapsed=0.4s rate=61572.1/s
[progress] 26800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26800) elapsed=0.4s rate=61605.5/s
[progress] 26900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26900) elapsed=0.4s rate=61649.2/s
[progress] 27000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27000) elapsed=0.4s rate=61677.6/s
[progress] 27100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27100) elapsed=0.4s rate=61706.5/s
[progress] 27200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27200) elapsed=0.4s rate=61731.0/s
[progress] 27300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27300) elapsed=0.4s rate=61648.1/s
[progress] 27400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27400) elapsed=0.4s rate=61662.9/s
[chrom] chr16 done in 0.0s
[chrom] starting chr17
[progress] 27500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27500) elapsed=0.4s rate=61687.0/s
[progress] 27600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27600) elapsed=0.4s rate=61709.6/s
[progress] 27700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27700) elapsed=0.4s rate=61728.1/s
[progress] 27800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27800) elapsed=0.5s rate=61776.8/s
[progress] 27900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27900) elapsed=0.5s rate=61794.5/s
[progress] 28000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28000) elapsed=0.5s rate=61819.7/s
[progress] 28100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28100) elapsed=0.5s rate=61723.1/s
[progress] 28200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28200) elapsed=0.5s rate=61764.3/s
[progress] 28300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28300) elapsed=0.5s rate=61796.7/s
[progress] 28400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28400) elapsed=0.5s rate=61808.8/s
[progress] 28500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28500) elapsed=0.5s rate=61839.2/s
[progress] 28600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28600) elapsed=0.5s rate=61852.3/s
[progress] 28700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28700) elapsed=0.5s rate=61876.8/s
[progress] 28800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28800) elapsed=0.5s rate=61864.0/s
[progress] 28900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28900) elapsed=0.5s rate=61896.8/s
[progress] 29000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29000) elapsed=0.5s rate=61924.0/s
[progress] 29100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29100) elapsed=0.5s rate=61949.9/s
[progress] 29200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29200) elapsed=0.5s rate=61966.1/s
[progress] 29300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29300) elapsed=0.5s rate=62004.7/s
[progress] 29400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29400) elapsed=0.5s rate=61198.4/s
[progress] 29500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29500) elapsed=0.5s rate=61232.5/s
[progress] 29600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29600) elapsed=0.5s rate=61158.0/s
[progress] 29700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29700) elapsed=0.5s rate=61169.1/s
[progress] 29800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29800) elapsed=0.5s rate=61179.9/s
[progress] 29900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29900) elapsed=0.5s rate=61207.1/s
[chrom] chr17 done in 0.0s
[chrom] starting chr18
[progress] 30000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30000) elapsed=0.5s rate=61232.7/s
[progress] 30100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30100) elapsed=0.5s rate=61225.9/s
[progress] 30200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30200) elapsed=0.5s rate=61256.4/s
[progress] 30300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30300) elapsed=0.5s rate=61227.6/s
[progress] 30400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30400) elapsed=0.5s rate=61225.4/s
[chrom] chr18 done in 0.0s
[chrom] starting chr19
[progress] 30500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30500) elapsed=0.5s rate=61245.1/s
[progress] 30600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30600) elapsed=0.5s rate=61274.6/s
[progress] 30700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30700) elapsed=0.5s rate=61292.5/s
[progress] 30800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30800) elapsed=0.5s rate=61306.4/s
[progress] 30900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30900) elapsed=0.5s rate=61243.9/s
[progress] 31000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=31000) elapsed=0.5s rate=61253.3/s
[progress] 31100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=31100) elapsed=0.5s rate=61267.1/s
[progress] 31200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=31200) elapsed=0.5s rate=61302.0/s
[progress] 31300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=31300) elapsed=0.5s rate=61335.9/s
[progress] 31400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=31400) elapsed=0.5s rate=61338.7/s
[progress] 31500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=31500) elapsed=0.5s rate=61353.4/s
[progress] 31600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=31600) elapsed=0.5s rate=61367.2/s
[progress] 31700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=31700) elapsed=0.5s rate=61333.6/s
[progress] 31800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=31800) elapsed=0.5s rate=61347.5/s
[progress] 31900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=31900) elapsed=0.5s rate=61357.7/s
[progress] 32000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=32000) elapsed=0.5s rate=61362.7/s
[progress] 32100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=32100) elapsed=0.5s rate=61399.0/s
[progress] 32200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=32200) elapsed=0.5s rate=61414.6/s
[progress] 32300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=32300) elapsed=0.5s rate=61365.8/s
[progress] 32400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=32400) elapsed=0.5s rate=61383.2/s
[progress] 32500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=32500) elapsed=0.5s rate=61403.4/s
[progress] 32600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=32600) elapsed=0.5s rate=61435.4/s
[progress] 32700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=32700) elapsed=0.5s rate=61441.3/s
[progress] 32800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=32800) elapsed=0.5s rate=61458.7/s
[progress] 32900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=32900) elapsed=0.5s rate=61364.1/s
[progress] 33000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=33000) elapsed=0.5s rate=61379.1/s
[progress] 33100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=33100) elapsed=0.5s rate=61406.3/s
[progress] 33200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=33200) elapsed=0.5s rate=61439.7/s
[progress] 33300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=33300) elapsed=0.5s rate=61470.1/s
[chrom] chr19 done in 0.0s
[chrom] starting chr20
[progress] 33400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=33400) elapsed=0.5s rate=61487.4/s
[progress] 33500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=33500) elapsed=0.5s rate=61509.1/s
[progress] 33600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=33600) elapsed=0.5s rate=61525.5/s
[progress] 33700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=33700) elapsed=0.5s rate=61457.4/s
[progress] 33800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=33800) elapsed=0.5s rate=61495.4/s
[progress] 33900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=33900) elapsed=0.6s rate=61525.4/s
[progress] 34000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=34000) elapsed=0.6s rate=61554.7/s
[progress] 34100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=34100) elapsed=0.6s rate=61589.2/s
[progress] 34200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=34200) elapsed=0.6s rate=61611.5/s
[progress] 34300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=34300) elapsed=0.6s rate=61641.5/s
[progress] 34400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=34400) elapsed=0.6s rate=61665.5/s
[chrom] chr20 done in 0.0s
[chrom] starting chr21
[progress] 34500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=34500) elapsed=0.6s rate=61688.3/s
[progress] 34600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=34600) elapsed=0.6s rate=61647.2/s
[progress] 34700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=34700) elapsed=0.6s rate=61671.3/s
[progress] 34800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=34800) elapsed=0.6s rate=61691.1/s
[chrom] chr21 done in 0.0s
[chrom] starting chr22
[progress] 34900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=34900) elapsed=0.6s rate=61710.9/s
[progress] 35000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=35000) elapsed=0.6s rate=61733.3/s
[progress] 35100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=35100) elapsed=0.6s rate=61761.8/s
[progress] 35200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=35200) elapsed=0.6s rate=61788.4/s
[progress] 35300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=35300) elapsed=0.6s rate=61743.4/s
[progress] 35400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=35400) elapsed=0.6s rate=61755.5/s
[progress] 35500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=35500) elapsed=0.6s rate=61768.8/s
[progress] 35600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=35600) elapsed=0.6s rate=61787.4/s
[progress] 35700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=35700) elapsed=0.6s rate=61804.8/s
[progress] 35800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=35800) elapsed=0.6s rate=61820.7/s
[progress] 35900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=35900) elapsed=0.6s rate=61844.2/s
[chrom] chr22 done in 0.0s
[chrom] starting chrX
[progress] 36000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=36000) elapsed=0.6s rate=61864.5/s
[progress] 36100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=36100) elapsed=0.6s rate=61839.4/s
[progress] 36200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=36200) elapsed=0.6s rate=61872.6/s
[progress] 36300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=36300) elapsed=0.6s rate=61891.4/s
[progress] 36400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=36400) elapsed=0.6s rate=61914.0/s
[progress] 36500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=36500) elapsed=0.6s rate=61948.7/s
[progress] 36600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=36600) elapsed=0.6s rate=61971.7/s
[progress] 36700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=36700) elapsed=0.6s rate=61985.1/s
[progress] 36800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=36800) elapsed=0.6s rate=62009.5/s
[progress] 36900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=36900) elapsed=0.6s rate=62025.9/s
[progress] 37000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=37000) elapsed=0.6s rate=62047.8/s
[progress] 37100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=37100) elapsed=0.6s rate=62075.9/s
[progress] 37200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=37200) elapsed=0.6s rate=62102.7/s
[progress] 37300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=37300) elapsed=0.6s rate=62122.7/s
[progress] 37400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=37400) elapsed=0.6s rate=62151.9/s
[progress] 37500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=37500) elapsed=0.6s rate=62183.8/s
[chrom] chrX done in 0.0s
[chrom] starting chrY
[chrom] chrY done in 0.0s
[done] 37526 variants in 0.6s (ok=0 no_reads=0 ref_mismatch=0 other=37526)