Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/e2d5b49478521212bf862e085cc4ab/.command.sh
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/targets/HG02657_x_HG02682_FF_5.targets.tsv
  Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/vcfs/HG02657_x_HG02682_FF_5.vcf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/e2d5b49478521212bf862e085cc4ab/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/6459dcd5ba53de0788476a9edab6db/HG02657_x_HG02682_FF_5.mix.bam
==> STAGING COMPLETE (7 inputs)

[init] ff = 0.050
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG02657_x_HG02682_FF_5.mix.bam
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 23098 sites
[chrom] starting chr1
[progress] 100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=100) elapsed=0.0s rate=28387.8/s
[progress] 200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=200) elapsed=0.0s rate=28217.9/s
[progress] 300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=300) elapsed=0.0s rate=27050.1/s
[progress] 400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=400) elapsed=0.0s rate=30283.2/s
[progress] 500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=500) elapsed=0.0s rate=29812.4/s
[progress] 600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=600) elapsed=0.0s rate=31963.1/s
[progress] 700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=700) elapsed=0.0s rate=33751.5/s
[progress] 800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=800) elapsed=0.0s rate=35537.8/s
[progress] 900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=900) elapsed=0.0s rate=34224.0/s
[progress] 1000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1000) elapsed=0.0s rate=35226.4/s
[progress] 1100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1100) elapsed=0.0s rate=36288.3/s
[progress] 1200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1200) elapsed=0.0s rate=37761.3/s
[progress] 1300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1300) elapsed=0.0s rate=38816.5/s
[progress] 1400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1400) elapsed=0.0s rate=39840.6/s
[progress] 1500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1500) elapsed=0.0s rate=39169.6/s
[progress] 1600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1600) elapsed=0.0s rate=40275.1/s
[progress] 1700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1700) elapsed=0.0s rate=41115.6/s
[progress] 1800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1800) elapsed=0.0s rate=41859.3/s
[progress] 1900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1900) elapsed=0.0s rate=42177.9/s
[progress] 2000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2000) elapsed=0.0s rate=40931.0/s
[progress] 2100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2100) elapsed=0.1s rate=41311.4/s
[progress] 2200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2200) elapsed=0.1s rate=41623.9/s
[progress] 2300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2300) elapsed=0.1s rate=41924.8/s
[progress] 2400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2400) elapsed=0.1s rate=41178.7/s
[progress] 2500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2500) elapsed=0.1s rate=41530.7/s
[chrom] chr1 done in 0.1s
[chrom] starting chr2
[progress] 2600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2600) elapsed=0.1s rate=41919.5/s
[progress] 2700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2700) elapsed=0.1s rate=42156.5/s
[progress] 2800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2800) elapsed=0.1s rate=41134.7/s
[progress] 2900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2900) elapsed=0.1s rate=41569.5/s
[progress] 3000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3000) elapsed=0.1s rate=41809.0/s
[progress] 3100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3100) elapsed=0.1s rate=42042.7/s
[progress] 3200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3200) elapsed=0.1s rate=41387.3/s
[progress] 3300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3300) elapsed=0.1s rate=41500.7/s
[progress] 3400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3400) elapsed=0.1s rate=41765.5/s
[progress] 3500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3500) elapsed=0.1s rate=42102.3/s
[progress] 3600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3600) elapsed=0.1s rate=41425.0/s
[progress] 3700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3700) elapsed=0.1s rate=41637.8/s
[chrom] chr2 done in 0.0s
[chrom] starting chr3
[progress] 3800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3800) elapsed=0.1s rate=41778.6/s
[progress] 3900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=3900) elapsed=0.1s rate=40969.4/s
[progress] 4000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4000) elapsed=0.1s rate=41276.6/s
[progress] 4100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4100) elapsed=0.1s rate=41592.0/s
[progress] 4200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4200) elapsed=0.1s rate=41809.8/s
[progress] 4300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4300) elapsed=0.1s rate=41942.1/s
[progress] 4400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4400) elapsed=0.1s rate=41343.8/s
[progress] 4500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4500) elapsed=0.1s rate=41507.9/s
[progress] 4600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4600) elapsed=0.1s rate=41687.9/s
[progress] 4700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4700) elapsed=0.1s rate=41317.6/s
[chrom] chr3 done in 0.0s
[chrom] starting chr4
[progress] 4800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4800) elapsed=0.1s rate=41602.2/s
[progress] 4900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4900) elapsed=0.1s rate=41775.6/s
[progress] 5000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5000) elapsed=0.1s rate=41899.8/s
[progress] 5100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5100) elapsed=0.1s rate=41449.9/s
[progress] 5200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5200) elapsed=0.1s rate=41745.5/s
[progress] 5300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5300) elapsed=0.1s rate=41821.7/s
[progress] 5400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5400) elapsed=0.1s rate=41956.9/s
[chrom] chr4 done in 0.0s
[chrom] starting chr5
[progress] 5500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5500) elapsed=0.1s rate=41437.8/s
[progress] 5600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5600) elapsed=0.1s rate=41604.6/s
[progress] 5700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5700) elapsed=0.1s rate=41728.0/s
[progress] 5800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5800) elapsed=0.1s rate=41920.1/s
[progress] 5900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5900) elapsed=0.1s rate=41652.9/s
[progress] 6000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6000) elapsed=0.1s rate=41824.2/s
[progress] 6100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6100) elapsed=0.1s rate=42003.2/s
[progress] 6200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6200) elapsed=0.1s rate=42153.9/s
[chrom] chr5 done in 0.0s
[chrom] starting chr6
[progress] 6300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6300) elapsed=0.1s rate=42294.1/s
[progress] 6400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6400) elapsed=0.2s rate=41943.0/s
[progress] 6500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6500) elapsed=0.2s rate=42118.8/s
[progress] 6600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6600) elapsed=0.2s rate=42356.2/s
[progress] 6700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6700) elapsed=0.2s rate=42569.3/s
[progress] 6800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6800) elapsed=0.2s rate=42830.6/s
[progress] 6900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6900) elapsed=0.2s rate=42276.7/s
[progress] 7000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7000) elapsed=0.2s rate=42349.0/s
[progress] 7100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7100) elapsed=0.2s rate=42444.1/s
[progress] 7200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7200) elapsed=0.2s rate=42549.1/s
[progress] 7300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7300) elapsed=0.2s rate=42228.3/s
[progress] 7400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7400) elapsed=0.2s rate=42379.8/s
[progress] 7500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7500) elapsed=0.2s rate=42455.2/s
[chrom] chr6 done in 0.0s
[chrom] starting chr7
[progress] 7600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7600) elapsed=0.2s rate=42561.2/s
[progress] 7700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7700) elapsed=0.2s rate=42280.6/s
[progress] 7800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7800) elapsed=0.2s rate=42394.2/s
[progress] 7900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7900) elapsed=0.2s rate=42447.7/s
[progress] 8000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8000) elapsed=0.2s rate=42559.5/s
[progress] 8100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8100) elapsed=0.2s rate=42265.8/s
[progress] 8200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8200) elapsed=0.2s rate=42401.4/s
[progress] 8300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8300) elapsed=0.2s rate=42420.4/s
[progress] 8400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8400) elapsed=0.2s rate=42551.5/s
[progress] 8500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8500) elapsed=0.2s rate=42705.6/s
[progress] 8600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8600) elapsed=0.2s rate=42486.7/s
[progress] 8700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8700) elapsed=0.2s rate=42532.1/s
[progress] 8800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8800) elapsed=0.2s rate=42574.3/s
[progress] 8900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8900) elapsed=0.2s rate=42703.7/s
[chrom] chr7 done in 0.0s
[chrom] starting chr8
[progress] 9000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9000) elapsed=0.2s rate=42419.3/s
[progress] 9100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9100) elapsed=0.2s rate=42470.7/s
[progress] 9200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9200) elapsed=0.2s rate=42588.4/s
[progress] 9300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9300) elapsed=0.2s rate=42699.4/s
[progress] 9400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9400) elapsed=0.2s rate=42523.5/s
[progress] 9500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9500) elapsed=0.2s rate=42669.5/s
[progress] 9600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9600) elapsed=0.2s rate=42814.7/s
[chrom] chr8 done in 0.0s
[chrom] starting chr9
[progress] 9700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9700) elapsed=0.2s rate=42922.1/s
[progress] 9800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9800) elapsed=0.2s rate=42674.0/s
[progress] 9900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9900) elapsed=0.2s rate=42765.4/s
[progress] 10000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10000) elapsed=0.2s rate=42868.4/s
[progress] 10100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10100) elapsed=0.2s rate=42906.4/s
[progress] 10200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10200) elapsed=0.2s rate=42605.0/s
[progress] 10300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10300) elapsed=0.2s rate=42683.5/s
[chrom] chr9 done in 0.0s
[chrom] starting chr10
[progress] 10400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10400) elapsed=0.2s rate=42772.7/s
[progress] 10500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10500) elapsed=0.2s rate=42878.7/s
[progress] 10600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10600) elapsed=0.2s rate=42690.3/s
[progress] 10700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10700) elapsed=0.3s rate=42753.4/s
[progress] 10800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10800) elapsed=0.3s rate=42825.7/s
[progress] 10900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10900) elapsed=0.3s rate=42931.1/s
[progress] 11000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11000) elapsed=0.3s rate=43025.8/s
[chrom] chr10 done in 0.0s
[chrom] starting chr11
[progress] 11100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11100) elapsed=0.3s rate=42846.8/s
[progress] 11200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11200) elapsed=0.3s rate=42932.6/s
[progress] 11300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11300) elapsed=0.3s rate=43021.4/s
[progress] 11400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11400) elapsed=0.3s rate=43154.5/s
[progress] 11500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11500) elapsed=0.3s rate=43282.9/s
[progress] 11600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11600) elapsed=0.3s rate=43086.7/s
[progress] 11700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11700) elapsed=0.3s rate=43133.1/s
[progress] 11800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11800) elapsed=0.3s rate=43188.4/s
[progress] 11900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11900) elapsed=0.3s rate=42969.9/s
[progress] 12000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12000) elapsed=0.3s rate=43064.0/s
[progress] 12100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12100) elapsed=0.3s rate=43181.5/s
[progress] 12200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12200) elapsed=0.3s rate=43279.9/s
[progress] 12300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12300) elapsed=0.3s rate=43366.8/s
[progress] 12400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12400) elapsed=0.3s rate=43207.4/s
[progress] 12500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12500) elapsed=0.3s rate=43256.7/s
[progress] 12600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12600) elapsed=0.3s rate=43355.7/s
[progress] 12700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12700) elapsed=0.3s rate=43427.2/s
[chrom] chr11 done in 0.0s
[chrom] starting chr12
[progress] 12800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12800) elapsed=0.3s rate=43230.3/s
[progress] 12900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12900) elapsed=0.3s rate=43256.6/s
[progress] 13000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13000) elapsed=0.3s rate=43291.1/s
[progress] 13100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13100) elapsed=0.3s rate=43406.0/s
[progress] 13200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13200) elapsed=0.3s rate=43473.8/s
[progress] 13300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13300) elapsed=0.3s rate=43315.9/s
[progress] 13400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13400) elapsed=0.3s rate=43360.0/s
[progress] 13500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13500) elapsed=0.3s rate=43418.8/s
[progress] 13600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13600) elapsed=0.3s rate=43451.4/s
[progress] 13700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13700) elapsed=0.3s rate=43281.9/s
[progress] 13800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13800) elapsed=0.3s rate=43335.4/s
[chrom] chr12 done in 0.0s
[chrom] starting chr13
[progress] 13900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13900) elapsed=0.3s rate=43402.0/s
[progress] 14000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14000) elapsed=0.3s rate=43471.6/s
[progress] 14100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14100) elapsed=0.3s rate=43324.8/s
[chrom] chr13 done in 0.0s
[chrom] starting chr14
[progress] 14200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14200) elapsed=0.3s rate=43371.3/s
[progress] 14300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14300) elapsed=0.3s rate=43419.4/s
[progress] 14400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14400) elapsed=0.3s rate=43453.3/s
[progress] 14500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14500) elapsed=0.3s rate=43295.1/s
[progress] 14600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14600) elapsed=0.3s rate=43353.9/s
[progress] 14700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14700) elapsed=0.3s rate=43451.0/s
[progress] 14800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14800) elapsed=0.3s rate=43559.9/s
[progress] 14900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14900) elapsed=0.3s rate=43644.3/s
[chrom] chr14 done in 0.0s
[chrom] starting chr15
[progress] 15000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15000) elapsed=0.3s rate=43725.4/s
[progress] 15100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15100) elapsed=0.3s rate=43614.1/s
[progress] 15200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15200) elapsed=0.3s rate=43660.8/s
[progress] 15300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15300) elapsed=0.4s rate=43710.9/s
[progress] 15400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15400) elapsed=0.4s rate=43780.7/s
[progress] 15500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15500) elapsed=0.4s rate=43821.7/s
[chrom] chr15 done in 0.0s
[chrom] starting chr16
[progress] 15600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15600) elapsed=0.4s rate=43724.9/s
[progress] 15700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15700) elapsed=0.4s rate=43787.4/s
[progress] 15800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15800) elapsed=0.4s rate=43867.8/s
[progress] 15900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15900) elapsed=0.4s rate=43920.6/s
[progress] 16000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16000) elapsed=0.4s rate=43832.2/s
[progress] 16100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16100) elapsed=0.4s rate=43923.7/s
[progress] 16200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16200) elapsed=0.4s rate=43963.6/s
[progress] 16300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16300) elapsed=0.4s rate=44054.0/s
[progress] 16400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16400) elapsed=0.4s rate=44096.7/s
[progress] 16500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16500) elapsed=0.4s rate=43985.6/s
[chrom] chr16 done in 0.0s
[chrom] starting chr17
[progress] 16600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16600) elapsed=0.4s rate=44036.0/s
[progress] 16700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16700) elapsed=0.4s rate=44100.0/s
[progress] 16800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16800) elapsed=0.4s rate=44169.5/s
[progress] 16900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16900) elapsed=0.4s rate=44232.5/s
[progress] 17000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17000) elapsed=0.4s rate=44210.4/s
[progress] 17100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17100) elapsed=0.4s rate=44243.9/s
[progress] 17200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17200) elapsed=0.4s rate=44306.4/s
[progress] 17300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17300) elapsed=0.4s rate=44393.5/s
[progress] 17400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17400) elapsed=0.4s rate=44462.6/s
[progress] 17500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17500) elapsed=0.4s rate=44387.0/s
[progress] 17600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17600) elapsed=0.4s rate=44454.8/s
[progress] 17700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17700) elapsed=0.4s rate=44493.0/s
[progress] 17800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17800) elapsed=0.4s rate=44538.2/s
[progress] 17900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17900) elapsed=0.4s rate=44450.2/s
[chrom] chr17 done in 0.0s
[chrom] starting chr18
[progress] 18000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18000) elapsed=0.4s rate=44489.6/s
[progress] 18100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18100) elapsed=0.4s rate=44519.0/s
[progress] 18200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18200) elapsed=0.4s rate=44563.5/s
[chrom] chr18 done in 0.0s
[chrom] starting chr19
[progress] 18300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18300) elapsed=0.4s rate=44475.6/s
[progress] 18400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18400) elapsed=0.4s rate=44535.3/s
[progress] 18500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18500) elapsed=0.4s rate=44585.0/s
[progress] 18600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18600) elapsed=0.4s rate=44632.8/s
[progress] 18700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18700) elapsed=0.4s rate=44584.6/s
[progress] 18800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18800) elapsed=0.4s rate=44637.8/s
[progress] 18900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18900) elapsed=0.4s rate=44681.3/s
[progress] 19000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19000) elapsed=0.4s rate=44759.4/s
[progress] 19100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19100) elapsed=0.4s rate=44829.5/s
[progress] 19200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19200) elapsed=0.4s rate=44865.8/s
[progress] 19300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19300) elapsed=0.4s rate=44813.0/s
[progress] 19400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19400) elapsed=0.4s rate=44867.0/s
[progress] 19500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19500) elapsed=0.4s rate=44934.1/s
[progress] 19600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19600) elapsed=0.4s rate=44992.5/s
[progress] 19700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19700) elapsed=0.4s rate=45048.6/s
[progress] 19800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19800) elapsed=0.4s rate=44987.1/s
[progress] 19900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19900) elapsed=0.4s rate=45056.9/s
[progress] 20000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20000) elapsed=0.4s rate=45109.8/s
[progress] 20100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20100) elapsed=0.4s rate=45161.1/s
[progress] 20200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20200) elapsed=0.4s rate=45219.7/s
[progress] 20300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20300) elapsed=0.4s rate=45276.2/s
[progress] 20400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20400) elapsed=0.5s rate=45190.1/s
[progress] 20500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20500) elapsed=0.5s rate=45216.4/s
[progress] 20600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20600) elapsed=0.5s rate=45265.4/s
[progress] 20700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20700) elapsed=0.5s rate=45332.5/s
[progress] 20800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20800) elapsed=0.5s rate=45412.0/s
[progress] 20900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20900) elapsed=0.5s rate=45489.2/s
[progress] 21000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21000) elapsed=0.5s rate=45501.4/s
[chrom] chr19 done in 0.1s
[chrom] starting chr20
[progress] 21100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21100) elapsed=0.5s rate=45549.5/s
[progress] 21200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21200) elapsed=0.5s rate=45594.9/s
[progress] 21300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21300) elapsed=0.5s rate=45642.5/s
[progress] 21400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21400) elapsed=0.5s rate=45686.7/s
[progress] 21500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21500) elapsed=0.5s rate=45577.5/s
[progress] 21600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21600) elapsed=0.5s rate=45604.8/s
[chrom] chr20 done in 0.0s
[chrom] starting chr21
[progress] 21700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21700) elapsed=0.5s rate=45643.9/s
[progress] 21800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21800) elapsed=0.5s rate=45688.1/s
[chrom] chr21 done in 0.0s
[chrom] starting chr22
[progress] 21900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21900) elapsed=0.5s rate=45737.5/s
[progress] 22000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22000) elapsed=0.5s rate=45660.3/s
[progress] 22100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22100) elapsed=0.5s rate=45708.4/s
[progress] 22200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22200) elapsed=0.5s rate=45739.2/s
[progress] 22300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22300) elapsed=0.5s rate=45789.0/s
[progress] 22400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22400) elapsed=0.5s rate=45738.4/s
[chrom] chr22 done in 0.0s
[chrom] starting chrX
[progress] 22500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22500) elapsed=0.5s rate=45767.3/s
[progress] 22600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22600) elapsed=0.5s rate=45817.3/s
[progress] 22700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22700) elapsed=0.5s rate=45853.0/s
[progress] 22800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22800) elapsed=0.5s rate=45906.7/s
[progress] 22900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22900) elapsed=0.5s rate=45959.7/s
[progress] 23000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23000) elapsed=0.5s rate=45982.7/s
[chrom] chrX done in 0.0s
[chrom] starting chrY
[progress] 23100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23100) elapsed=0.5s rate=46020.1/s
[chrom] chrY done in 0.0s
[done] 23100 variants in 0.5s (ok=0 no_reads=0 ref_mismatch=0 other=23100)