Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/targets/HG00621_x_HG00673_FF_5.targets.tsv Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/vcfs/HG00621_x_HG00673_FF_5.vcf Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/75fc7c21bb47210e2677cb38065bd2/.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/c7/75fc7c21bb47210e2677cb38065bd2/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/f23c34a4a4932755834603caa72795/HG00621_x_HG00673_FF_5.mix.bam ==> STAGING COMPLETE (7 inputs) [init] ff = 0.050 [init] alphas = [0.012, 0.05, 0.1] [init] opening BAM HG00621_x_HG00673_FF_5.mix.bam [init] opening reference Homo_sapiens_assembly38.fasta [init] target list: 49188 sites [chrom] starting chr1 [progress] 100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=100) elapsed=0.0s rate=29645.9/s [progress] 200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=200) elapsed=0.0s rate=31624.1/s [progress] 300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=300) elapsed=0.0s rate=37727.6/s [progress] 400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=400) elapsed=0.0s rate=42545.1/s [progress] 500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=500) elapsed=0.0s rate=39429.8/s [progress] 600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=600) elapsed=0.0s rate=42229.5/s [progress] 700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=700) elapsed=0.0s rate=43826.3/s [progress] 800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=800) elapsed=0.0s rate=45955.5/s [progress] 900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=900) 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other=8300) elapsed=0.2s rate=54347.7/s [chrom] chr2 done in 0.1s [chrom] starting chr3 [progress] 8400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8400) elapsed=0.2s rate=53812.1/s [progress] 8500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8500) elapsed=0.2s rate=53950.9/s [progress] 8600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8600) elapsed=0.2s rate=54103.1/s [progress] 8700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8700) elapsed=0.2s rate=54230.6/s [progress] 8800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8800) elapsed=0.2s rate=54342.8/s [progress] 8900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8900) elapsed=0.2s rate=54428.0/s [progress] 9000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9000) elapsed=0.2s rate=54552.9/s [progress] 9100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9100) elapsed=0.2s rate=54689.0/s [progress] 9200 variants processed (ok=0 no_reads=0 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elapsed=0.2s rate=54280.0/s [progress] 10200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10200) elapsed=0.2s rate=54389.8/s [progress] 10300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10300) elapsed=0.2s rate=54460.3/s [progress] 10400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10400) elapsed=0.2s rate=54487.9/s [progress] 10500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10500) elapsed=0.2s rate=54549.1/s [progress] 10600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10600) elapsed=0.2s rate=53978.8/s [progress] 10700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10700) elapsed=0.2s rate=54066.9/s [progress] 10800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10800) elapsed=0.2s rate=54121.7/s [chrom] chr3 done in 0.0s [chrom] starting chr4 [progress] 10900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10900) elapsed=0.2s rate=54205.2/s [progress] 11000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11000) elapsed=0.2s rate=54277.6/s [progress] 11100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11100) elapsed=0.2s rate=54364.2/s [progress] 11200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11200) elapsed=0.2s rate=54457.9/s [progress] 11300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11300) elapsed=0.2s rate=54133.7/s [progress] 11400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11400) elapsed=0.2s rate=54170.7/s [progress] 11500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11500) elapsed=0.2s rate=54280.5/s [progress] 11600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11600) elapsed=0.2s rate=54397.8/s [progress] 11700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11700) elapsed=0.2s rate=54515.3/s [progress] 11800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11800) elapsed=0.2s rate=54631.4/s [progress] 11900 variants processed (ok=0 no_reads=0 ref_mismatch=0 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(ok=0 no_reads=0 ref_mismatch=0 other=18200) elapsed=0.3s rate=55570.0/s [progress] 18300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18300) elapsed=0.3s rate=55625.0/s [progress] 18400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18400) elapsed=0.3s rate=55658.2/s [progress] 18500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18500) elapsed=0.3s rate=55712.6/s [progress] 18600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18600) elapsed=0.3s rate=55774.9/s [progress] 18700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18700) elapsed=0.3s rate=55833.7/s [progress] 18800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18800) elapsed=0.3s rate=55861.5/s [progress] 18900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18900) elapsed=0.3s rate=55534.7/s [progress] 19000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19000) elapsed=0.3s rate=55574.8/s [progress] 19100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19100) elapsed=0.3s rate=55621.9/s [progress] 19200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19200) elapsed=0.3s rate=55682.8/s [progress] 19300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19300) elapsed=0.3s rate=55732.0/s [progress] 19400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19400) elapsed=0.3s rate=55785.1/s [progress] 19500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19500) elapsed=0.4s rate=55555.6/s [progress] 19600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19600) elapsed=0.4s rate=55605.9/s [progress] 19700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19700) elapsed=0.4s rate=55662.2/s [progress] 19800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19800) elapsed=0.4s rate=55699.6/s [progress] 19900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19900) elapsed=0.4s rate=55756.2/s [progress] 20000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20000) elapsed=0.4s rate=55795.6/s [progress] 20100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20100) elapsed=0.4s rate=55848.3/s [chrom] chr7 done in 0.0s [chrom] starting chr8 [progress] 20200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20200) elapsed=0.4s rate=55650.3/s [progress] 20300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20300) elapsed=0.4s rate=55689.0/s [progress] 20400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20400) elapsed=0.4s rate=55723.0/s [progress] 20500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20500) elapsed=0.4s rate=55778.0/s [progress] 20600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20600) elapsed=0.4s rate=55832.5/s [progress] 20700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20700) elapsed=0.4s rate=55873.5/s [progress] 20800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20800) elapsed=0.4s rate=55920.5/s [progress] 20900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20900) elapsed=0.4s rate=55977.8/s [progress] 21000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21000) elapsed=0.4s rate=55741.5/s [progress] 21100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21100) elapsed=0.4s rate=55780.5/s [progress] 21200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21200) elapsed=0.4s rate=55840.2/s [progress] 21300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21300) elapsed=0.4s rate=55877.2/s [progress] 21400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21400) elapsed=0.4s rate=55927.3/s [progress] 21500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21500) elapsed=0.4s rate=55970.5/s [progress] 21600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21600) elapsed=0.4s rate=56026.2/s [chrom] chr8 done in 0.0s [chrom] starting chr9 [progress] 21700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21700) elapsed=0.4s rate=56074.9/s [progress] 21800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21800) elapsed=0.4s rate=55896.9/s [progress] 21900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21900) elapsed=0.4s rate=55938.9/s [progress] 22000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22000) elapsed=0.4s rate=55991.8/s [progress] 22100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22100) elapsed=0.4s rate=56022.0/s [progress] 22200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22200) elapsed=0.4s rate=56062.2/s [progress] 22300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22300) elapsed=0.4s rate=56128.1/s [progress] 22400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22400) elapsed=0.4s rate=56180.3/s [progress] 22500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22500) elapsed=0.4s rate=55936.4/s [progress] 22600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22600) elapsed=0.4s rate=55979.8/s [progress] 22700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22700) elapsed=0.4s rate=56011.3/s [progress] 22800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22800) elapsed=0.4s rate=56057.4/s [progress] 22900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22900) elapsed=0.4s rate=56101.1/s [progress] 23000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23000) elapsed=0.4s rate=56152.5/s [progress] 23100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23100) elapsed=0.4s rate=56207.6/s [progress] 23200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23200) elapsed=0.4s rate=56252.5/s [progress] 23300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23300) elapsed=0.4s rate=56137.9/s [progress] 23400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23400) elapsed=0.4s rate=56191.8/s [progress] 23500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23500) elapsed=0.4s rate=56245.0/s [chrom] chr9 done in 0.0s [chrom] starting chr10 [progress] 23600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23600) elapsed=0.4s rate=56280.8/s [progress] 23700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23700) elapsed=0.4s rate=56337.6/s [progress] 23800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23800) elapsed=0.4s rate=56382.2/s [progress] 23900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23900) elapsed=0.4s rate=56438.2/s [progress] 24000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24000) elapsed=0.4s rate=56479.1/s [progress] 24100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24100) elapsed=0.4s rate=56389.7/s [progress] 24200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24200) elapsed=0.4s rate=56430.7/s [progress] 24300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24300) elapsed=0.4s rate=56468.5/s [progress] 24400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24400) elapsed=0.4s rate=56542.9/s [progress] 24500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24500) elapsed=0.4s rate=56586.2/s [progress] 24600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24600) elapsed=0.4s rate=56619.5/s [progress] 24700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24700) elapsed=0.4s rate=56677.2/s [progress] 24800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24800) elapsed=0.4s rate=56739.5/s [progress] 24900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=24900) elapsed=0.4s rate=56794.9/s [progress] 25000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25000) elapsed=0.4s rate=56657.8/s [progress] 25100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25100) elapsed=0.4s rate=56704.8/s [progress] 25200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25200) elapsed=0.4s rate=56738.2/s [chrom] chr10 done in 0.0s [chrom] starting chr11 [progress] 25300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25300) elapsed=0.4s rate=56769.1/s [progress] 25400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25400) elapsed=0.4s rate=56804.4/s [progress] 25500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25500) elapsed=0.4s rate=56823.8/s [progress] 25600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25600) elapsed=0.5s rate=56643.5/s [progress] 25700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25700) elapsed=0.5s rate=56681.8/s [progress] 25800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25800) elapsed=0.5s rate=56730.9/s [progress] 25900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=25900) elapsed=0.5s rate=56781.0/s [progress] 26000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26000) elapsed=0.5s rate=56801.6/s [progress] 26100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26100) elapsed=0.5s rate=56833.2/s [progress] 26200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26200) elapsed=0.5s rate=56871.2/s [progress] 26300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26300) elapsed=0.5s rate=56914.1/s [progress] 26400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26400) elapsed=0.5s rate=56955.6/s [progress] 26500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26500) elapsed=0.5s rate=56843.4/s [progress] 26600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26600) elapsed=0.5s rate=56891.8/s [progress] 26700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26700) elapsed=0.5s rate=56925.0/s [progress] 26800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26800) elapsed=0.5s rate=56948.7/s [progress] 26900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=26900) elapsed=0.5s rate=56976.9/s [progress] 27000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27000) elapsed=0.5s rate=57020.3/s [progress] 27100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27100) elapsed=0.5s rate=57062.4/s [progress] 27200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27200) elapsed=0.5s rate=56980.6/s [progress] 27300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27300) elapsed=0.5s rate=57019.8/s [progress] 27400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27400) elapsed=0.5s rate=57042.8/s [progress] 27500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27500) elapsed=0.5s rate=57090.2/s [progress] 27600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27600) elapsed=0.5s rate=57132.5/s [progress] 27700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27700) elapsed=0.5s rate=57178.1/s [progress] 27800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27800) elapsed=0.5s rate=57207.4/s [progress] 27900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=27900) elapsed=0.5s rate=57238.3/s [progress] 28000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28000) elapsed=0.5s rate=57282.5/s [progress] 28100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28100) elapsed=0.5s rate=57109.8/s [progress] 28200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28200) elapsed=0.5s rate=57164.5/s [progress] 28300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28300) elapsed=0.5s rate=57198.7/s [progress] 28400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28400) elapsed=0.5s rate=57223.3/s [progress] 28500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28500) elapsed=0.5s rate=57264.9/s [progress] 28600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28600) elapsed=0.5s rate=57301.0/s [progress] 28700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28700) elapsed=0.5s rate=57306.5/s [chrom] chr11 done in 0.1s [chrom] starting chr12 [progress] 28800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28800) elapsed=0.5s rate=57225.8/s [progress] 28900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=28900) elapsed=0.5s rate=57266.8/s [progress] 29000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29000) elapsed=0.5s rate=57300.1/s [progress] 29100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29100) elapsed=0.5s rate=57291.2/s [progress] 29200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29200) elapsed=0.5s rate=57315.7/s [progress] 29300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29300) elapsed=0.5s rate=57340.6/s [progress] 29400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29400) elapsed=0.5s rate=57202.1/s [progress] 29500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29500) elapsed=0.5s rate=57232.7/s [progress] 29600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29600) elapsed=0.5s rate=57265.6/s [progress] 29700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29700) elapsed=0.5s rate=57312.0/s [progress] 29800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29800) elapsed=0.5s rate=57338.3/s [progress] 29900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=29900) elapsed=0.5s rate=57383.1/s [progress] 30000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30000) elapsed=0.5s rate=57416.5/s [progress] 30100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30100) elapsed=0.5s rate=57452.0/s [progress] 30200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30200) elapsed=0.5s rate=57484.1/s [progress] 30300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30300) elapsed=0.5s rate=57376.5/s [progress] 30400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30400) elapsed=0.5s rate=57412.8/s [progress] 30500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30500) elapsed=0.5s rate=57436.9/s [progress] 30600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30600) elapsed=0.5s rate=57478.7/s [progress] 30700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30700) elapsed=0.5s rate=57508.1/s [progress] 30800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30800) elapsed=0.5s rate=57532.9/s [progress] 30900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=30900) elapsed=0.5s rate=57560.1/s [progress] 31000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=31000) elapsed=0.5s rate=57431.8/s [chrom] chr12 done in 0.0s [chrom] starting chr13 [progress] 31100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=31100) elapsed=0.5s rate=57460.6/s [progress] 31200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=31200) elapsed=0.5s rate=57478.0/s [progress] 31300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=31300) elapsed=0.5s rate=57510.4/s [progress] 31400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=31400) elapsed=0.5s rate=57538.9/s [progress] 31500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=31500) elapsed=0.5s rate=57567.5/s [progress] 31600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=31600) elapsed=0.5s rate=57588.8/s [progress] 31700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=31700) elapsed=0.6s rate=57610.4/s [progress] 31800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=31800) elapsed=0.6s rate=57484.0/s [chrom] chr13 done in 0.0s [chrom] starting chr14 [progress] 31900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=31900) elapsed=0.6s rate=57445.1/s [progress] 32000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=32000) elapsed=0.6s rate=57449.2/s [progress] 32100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=32100) elapsed=0.6s rate=57450.1/s [progress] 32200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=32200) elapsed=0.6s rate=57453.8/s [progress] 32300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=32300) elapsed=0.6s rate=57456.2/s [progress] 32400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=32400) elapsed=0.6s rate=57441.4/s [progress] 32500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=32500) elapsed=0.6s rate=57445.2/s [progress] 32600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=32600) elapsed=0.6s rate=57255.2/s [progress] 32700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=32700) elapsed=0.6s rate=57281.0/s [progress] 32800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=32800) elapsed=0.6s rate=57307.0/s [progress] 32900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=32900) elapsed=0.6s rate=57305.9/s [progress] 33000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=33000) elapsed=0.6s rate=57282.3/s [progress] 33100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=33100) elapsed=0.6s rate=57289.8/s [progress] 33200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=33200) elapsed=0.6s rate=57243.5/s [chrom] chr14 done in 0.0s [chrom] starting chr15 [progress] 33300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=33300) elapsed=0.6s rate=57193.3/s [progress] 33400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=33400) elapsed=0.6s rate=56906.3/s [progress] 33500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=33500) elapsed=0.6s rate=56876.2/s [progress] 33600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=33600) elapsed=0.6s rate=56827.5/s [progress] 33700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=33700) elapsed=0.6s rate=56796.0/s [progress] 33800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=33800) elapsed=0.6s rate=56800.9/s [progress] 33900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=33900) elapsed=0.6s rate=56801.9/s [progress] 34000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=34000) elapsed=0.6s rate=56805.0/s [progress] 34100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=34100) elapsed=0.6s rate=56786.9/s [progress] 34200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=34200) elapsed=0.6s rate=56586.3/s [progress] 34300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=34300) elapsed=0.6s rate=56571.5/s [progress] 34400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=34400) elapsed=0.6s rate=56585.9/s [progress] 34500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=34500) elapsed=0.6s rate=56592.6/s [chrom] chr15 done in 0.0s [chrom] starting chr16 [progress] 34600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=34600) elapsed=0.6s rate=56616.9/s [progress] 34700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=34700) elapsed=0.6s rate=56625.6/s [progress] 34800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=34800) elapsed=0.6s rate=56640.2/s [progress] 34900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=34900) elapsed=0.6s rate=56662.8/s [progress] 35000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=35000) elapsed=0.6s rate=56548.4/s [progress] 35100 variants processed (ok=0 no_reads=0 ref_mismatch=0 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elapsed=0.6s rate=56223.2/s [progress] 36100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=36100) elapsed=0.6s rate=56199.2/s [progress] 36200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=36200) elapsed=0.6s rate=56177.3/s [progress] 36300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=36300) elapsed=0.6s rate=56145.3/s [progress] 36400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=36400) elapsed=0.6s rate=56125.5/s [progress] 36500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=36500) elapsed=0.7s rate=56070.0/s [progress] 36600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=36600) elapsed=0.7s rate=55879.6/s [progress] 36700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=36700) elapsed=0.7s rate=55861.1/s [progress] 36800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=36800) elapsed=0.7s rate=55813.8/s [chrom] chr16 done in 0.0s [chrom] starting chr17 [progress] 36900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=36900) elapsed=0.7s rate=55791.9/s [progress] 37000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=37000) elapsed=0.7s rate=55780.2/s [progress] 37100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=37100) elapsed=0.7s rate=55773.3/s [progress] 37200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=37200) elapsed=0.7s rate=55781.3/s [progress] 37300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=37300) elapsed=0.7s rate=55794.1/s [progress] 37400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=37400) elapsed=0.7s rate=55568.2/s [progress] 37500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=37500) elapsed=0.7s rate=55549.4/s [progress] 37600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=37600) elapsed=0.7s rate=55508.1/s [progress] 37700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=37700) elapsed=0.7s rate=55495.3/s [progress] 37800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=37800) elapsed=0.7s rate=55489.3/s [progress] 37900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=37900) elapsed=0.7s rate=55461.0/s [progress] 38000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=38000) elapsed=0.7s rate=55448.0/s [progress] 38100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=38100) elapsed=0.7s rate=55438.5/s [progress] 38200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=38200) elapsed=0.7s rate=55190.4/s [progress] 38300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=38300) elapsed=0.7s rate=55186.5/s [progress] 38400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=38400) elapsed=0.7s rate=55183.1/s [progress] 38500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=38500) elapsed=0.7s rate=55160.6/s [progress] 38600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=38600) elapsed=0.7s rate=55160.2/s [progress] 38700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=38700) elapsed=0.7s rate=55167.6/s [progress] 38800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=38800) elapsed=0.7s rate=55154.5/s [progress] 38900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=38900) elapsed=0.7s rate=54983.3/s [progress] 39000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=39000) elapsed=0.7s rate=54968.6/s [progress] 39100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=39100) elapsed=0.7s rate=54966.9/s [progress] 39200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=39200) elapsed=0.7s rate=54993.1/s [progress] 39300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=39300) elapsed=0.7s rate=55009.7/s [progress] 39400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=39400) elapsed=0.7s rate=55027.7/s [progress] 39500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=39500) elapsed=0.7s rate=55041.1/s [progress] 39600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=39600) elapsed=0.7s rate=55047.4/s [progress] 39700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=39700) elapsed=0.7s rate=55057.2/s [progress] 39800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=39800) elapsed=0.7s rate=55049.9/s [progress] 39900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=39900) elapsed=0.7s rate=54871.0/s [progress] 40000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=40000) elapsed=0.7s rate=54872.9/s [progress] 40100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=40100) elapsed=0.7s rate=54891.3/s [progress] 40200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=40200) elapsed=0.7s rate=54899.9/s [progress] 40300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=40300) elapsed=0.7s rate=54934.4/s [chrom] chr17 done in 0.1s [chrom] starting chr18 [progress] 40400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=40400) elapsed=0.7s rate=54953.4/s [progress] 40500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=40500) elapsed=0.7s rate=54969.2/s [progress] 40600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=40600) elapsed=0.7s rate=54889.7/s [progress] 40700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=40700) elapsed=0.7s rate=54917.0/s [progress] 40800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=40800) elapsed=0.7s rate=54946.4/s [progress] 40900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=40900) elapsed=0.7s rate=54965.8/s [chrom] chr18 done in 0.0s [chrom] starting chr19 [progress] 41000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=41000) elapsed=0.7s rate=54988.8/s [progress] 41100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=41100) elapsed=0.7s rate=55017.1/s [progress] 41200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=41200) elapsed=0.7s rate=55039.4/s [progress] 41300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=41300) elapsed=0.7s rate=55068.9/s [progress] 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processed (ok=0 no_reads=0 ref_mismatch=0 other=42300) elapsed=0.8s rate=55078.0/s [progress] 42400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=42400) elapsed=0.8s rate=55100.9/s [progress] 42500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=42500) elapsed=0.8s rate=55124.8/s [progress] 42600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=42600) elapsed=0.8s rate=55146.7/s [progress] 42700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=42700) elapsed=0.8s rate=55171.8/s [progress] 42800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=42800) elapsed=0.8s rate=55191.3/s [progress] 42900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=42900) elapsed=0.8s rate=55198.0/s [progress] 43000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=43000) elapsed=0.8s rate=55105.9/s [progress] 43100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=43100) elapsed=0.8s rate=55125.5/s [progress] 43200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=43200) elapsed=0.8s rate=55154.1/s [progress] 43300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=43300) elapsed=0.8s rate=55169.2/s [progress] 43400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=43400) elapsed=0.8s rate=55189.0/s [progress] 43500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=43500) elapsed=0.8s rate=55213.5/s [progress] 43600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=43600) elapsed=0.8s rate=55232.8/s [progress] 43700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=43700) elapsed=0.8s rate=55254.9/s [progress] 43800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=43800) elapsed=0.8s rate=55186.7/s [progress] 43900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=43900) elapsed=0.8s rate=55207.7/s [progress] 44000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=44000) elapsed=0.8s rate=55214.5/s [progress] 44100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=44100) elapsed=0.8s rate=55226.9/s [progress] 44200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=44200) elapsed=0.8s rate=55243.9/s [progress] 44300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=44300) elapsed=0.8s rate=55261.7/s [progress] 44400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=44400) elapsed=0.8s rate=55257.3/s [progress] 44500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=44500) elapsed=0.8s rate=55161.4/s [progress] 44600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=44600) elapsed=0.8s rate=55173.3/s [progress] 44700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=44700) elapsed=0.8s rate=55188.6/s [progress] 44800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=44800) elapsed=0.8s rate=55193.8/s [progress] 44900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=44900) elapsed=0.8s rate=55213.3/s [chrom] chr19 done in 0.1s [chrom] starting chr20 [progress] 45000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=45000) elapsed=0.8s rate=55224.4/s [progress] 45100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=45100) elapsed=0.8s rate=55248.0/s [progress] 45200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=45200) elapsed=0.8s rate=55267.8/s [progress] 45300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=45300) elapsed=0.8s rate=55193.1/s [progress] 45400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=45400) elapsed=0.8s rate=55208.4/s [progress] 45500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=45500) elapsed=0.8s rate=55236.1/s [progress] 45600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=45600) elapsed=0.8s rate=55258.4/s [progress] 45700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=45700) elapsed=0.8s rate=55276.8/s [progress] 45800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=45800) elapsed=0.8s rate=55298.1/s [progress] 45900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=45900) elapsed=0.8s rate=55285.9/s [progress] 46000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=46000) elapsed=0.8s rate=55264.9/s [progress] 46100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=46100) elapsed=0.8s rate=55246.7/s [progress] 46200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=46200) elapsed=0.8s rate=55117.4/s [progress] 46300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=46300) elapsed=0.8s rate=55112.5/s [chrom] chr20 done in 0.0s [chrom] starting chr21 [progress] 46400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=46400) elapsed=0.8s rate=55124.0/s [progress] 46500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=46500) elapsed=0.8s rate=55140.1/s [progress] 46600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=46600) elapsed=0.8s rate=55158.7/s [progress] 46700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=46700) elapsed=0.8s rate=55164.5/s [progress] 46800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=46800) elapsed=0.8s rate=55174.0/s [progress] 46900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=46900) elapsed=0.8s rate=55184.5/s [chrom] chr21 done in 0.0s [chrom] starting chr22 [progress] 47000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=47000) elapsed=0.9s rate=55198.4/s [progress] 47100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=47100) elapsed=0.9s rate=55096.6/s [progress] 47200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=47200) elapsed=0.9s rate=55093.4/s [progress] 47300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=47300) elapsed=0.9s rate=55077.2/s [progress] 47400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=47400) elapsed=0.9s rate=55060.1/s [progress] 47500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=47500) elapsed=0.9s rate=55055.2/s [progress] 47600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=47600) elapsed=0.9s rate=55040.8/s [progress] 47700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=47700) elapsed=0.9s rate=55025.4/s [progress] 47800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=47800) elapsed=0.9s rate=55016.3/s [progress] 47900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=47900) elapsed=0.9s rate=55020.5/s [progress] 48000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=48000) elapsed=0.9s rate=54906.7/s [progress] 48100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=48100) elapsed=0.9s rate=54922.3/s [progress] 48200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=48200) elapsed=0.9s rate=54939.7/s [progress] 48300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=48300) elapsed=0.9s rate=54960.6/s [chrom] chr22 done in 0.0s [chrom] starting chrX [progress] 48400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=48400) elapsed=0.9s rate=54978.1/s [progress] 48500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=48500) elapsed=0.9s rate=54993.7/s [progress] 48600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=48600) elapsed=0.9s rate=55009.3/s [progress] 48700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=48700) elapsed=0.9s rate=55023.3/s [progress] 48800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=48800) elapsed=0.9s rate=55031.6/s [progress] 48900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=48900) elapsed=0.9s rate=55045.1/s [progress] 49000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=49000) elapsed=0.9s rate=55045.6/s [progress] 49100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=49100) elapsed=0.9s rate=55057.1/s [chrom] chrX done in 0.0s [chrom] starting chrY [chrom] chrY done in 0.0s [done] 49190 variants in 0.9s (ok=0 no_reads=0 ref_mismatch=0 other=49190)