Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/b2ae160ef8bef6a83bdfbbfe7421c9/.command.sh 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/HG02855_x_HG02886_FF_10.vcf Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/786a2804e7f371871722930058fa5c/HG02855_x_HG02886_FF_10.mix.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/b2ae160ef8bef6a83bdfbbfe7421c9/.command.run Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/targets/HG02855_x_HG02886_FF_10.targets.tsv ==> STAGING COMPLETE (7 inputs) [init] ff = 0.100 [init] alphas = [0.012, 0.05, 0.1] [init] opening BAM HG02855_x_HG02886_FF_10.mix.bam [init] opening reference Homo_sapiens_assembly38.fasta [init] target list: 23548 sites [chrom] starting chr1 [progress] 100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=100) elapsed=0.0s rate=25088.6/s [progress] 200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=200) elapsed=0.0s rate=30389.1/s [progress] 300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=300) elapsed=0.0s rate=27270.0/s [progress] 400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=400) elapsed=0.0s rate=29676.3/s [progress] 500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=500) elapsed=0.0s rate=32456.1/s [progress] 600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=600) elapsed=0.0s rate=33480.8/s [progress] 700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=700) elapsed=0.0s rate=35301.3/s [progress] 800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=800) elapsed=0.0s rate=36961.5/s [progress] 900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=900) 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[progress] 1900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=1900) elapsed=0.0s rate=44931.7/s [progress] 2000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2000) elapsed=0.0s rate=45420.4/s [progress] 2100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2100) elapsed=0.0s rate=45020.7/s [progress] 2200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2200) elapsed=0.0s rate=45487.1/s [chrom] chr1 done in 0.0s [chrom] starting chr2 [progress] 2300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2300) elapsed=0.1s rate=45702.6/s [progress] 2400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2400) elapsed=0.1s rate=46174.8/s [progress] 2500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2500) elapsed=0.1s rate=46521.5/s [progress] 2600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2600) elapsed=0.1s rate=45596.4/s [progress] 2700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=2700) elapsed=0.1s 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[progress] 4600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4600) elapsed=0.1s rate=47926.9/s [chrom] chr3 done in 0.0s [chrom] starting chr4 [progress] 4700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4700) elapsed=0.1s rate=48023.3/s [progress] 4800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4800) elapsed=0.1s rate=48222.2/s [progress] 4900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=4900) elapsed=0.1s rate=48088.9/s [progress] 5000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5000) elapsed=0.1s rate=48247.0/s [progress] 5100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5100) elapsed=0.1s rate=48391.3/s [progress] 5200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5200) elapsed=0.1s rate=48604.0/s [progress] 5300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5300) elapsed=0.1s rate=48713.9/s [progress] 5400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5400) elapsed=0.1s rate=48347.4/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=48368.6/s [progress] 5600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5600) elapsed=0.1s rate=48390.9/s [progress] 5700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5700) elapsed=0.1s rate=48578.8/s [progress] 5800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5800) elapsed=0.1s rate=48209.4/s [progress] 5900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=5900) elapsed=0.1s rate=48356.6/s [progress] 6000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6000) elapsed=0.1s rate=48475.1/s [progress] 6100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6100) elapsed=0.1s rate=48580.3/s [chrom] chr5 done in 0.0s [chrom] starting chr6 [progress] 6200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6200) elapsed=0.1s rate=48321.4/s [progress] 6300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6300) elapsed=0.1s rate=48427.0/s [progress] 6400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6400) elapsed=0.1s rate=48564.2/s [progress] 6500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6500) elapsed=0.1s rate=48765.7/s [progress] 6600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6600) elapsed=0.1s rate=48879.1/s [progress] 6700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6700) elapsed=0.1s rate=48712.9/s [progress] 6800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6800) elapsed=0.1s rate=48758.0/s [progress] 6900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=6900) elapsed=0.1s rate=48872.4/s [progress] 7000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7000) elapsed=0.1s rate=48972.3/s [progress] 7100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7100) elapsed=0.1s rate=49109.2/s [progress] 7200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7200) elapsed=0.1s rate=48795.6/s [progress] 7300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7300) elapsed=0.1s rate=48819.3/s [chrom] chr6 done in 0.0s [chrom] starting chr7 [progress] 7400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7400) elapsed=0.2s rate=48936.4/s [progress] 7500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7500) elapsed=0.2s rate=49050.2/s [progress] 7600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7600) elapsed=0.2s rate=49142.6/s [progress] 7700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7700) elapsed=0.2s rate=49035.9/s [progress] 7800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7800) elapsed=0.2s rate=49112.7/s [progress] 7900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=7900) elapsed=0.2s rate=49210.7/s [progress] 8000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8000) elapsed=0.2s rate=49298.7/s [progress] 8100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8100) elapsed=0.2s rate=49077.7/s [progress] 8200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8200) elapsed=0.2s rate=49005.4/s [progress] 8300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8300) elapsed=0.2s rate=49115.6/s [progress] 8400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8400) elapsed=0.2s rate=49253.2/s [progress] 8500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8500) elapsed=0.2s rate=49318.3/s [progress] 8600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8600) elapsed=0.2s rate=49116.0/s [progress] 8700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8700) elapsed=0.2s rate=49243.1/s [progress] 8800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8800) elapsed=0.2s rate=49348.8/s [chrom] chr7 done in 0.0s [chrom] starting chr8 [progress] 8900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=8900) elapsed=0.2s rate=49454.8/s [progress] 9000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9000) elapsed=0.2s rate=49458.3/s [progress] 9100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9100) elapsed=0.2s rate=49343.8/s [progress] 9200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9200) elapsed=0.2s rate=49471.1/s [progress] 9300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9300) elapsed=0.2s rate=49512.7/s [progress] 9400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9400) elapsed=0.2s rate=49585.7/s [progress] 9500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9500) elapsed=0.2s rate=49717.8/s [chrom] chr8 done in 0.0s [chrom] starting chr9 [progress] 9600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9600) elapsed=0.2s rate=49652.5/s [progress] 9700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9700) elapsed=0.2s rate=49733.8/s [progress] 9800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9800) elapsed=0.2s rate=49731.6/s [progress] 9900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=9900) elapsed=0.2s rate=49801.6/s [progress] 10000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10000) elapsed=0.2s rate=49875.4/s [progress] 10100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10100) elapsed=0.2s rate=49540.7/s [progress] 10200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10200) elapsed=0.2s rate=49619.8/s [progress] 10300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10300) elapsed=0.2s rate=49680.9/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=49735.6/s [progress] 10500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10500) elapsed=0.2s rate=49593.6/s [progress] 10600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10600) elapsed=0.2s rate=49650.3/s [progress] 10700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10700) elapsed=0.2s rate=49728.8/s [progress] 10800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10800) elapsed=0.2s rate=49740.6/s [progress] 10900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=10900) elapsed=0.2s rate=49814.5/s [progress] 11000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11000) elapsed=0.2s rate=49695.2/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=0.2s rate=49692.7/s [progress] 11200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11200) elapsed=0.2s rate=49730.0/s [progress] 11300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11300) elapsed=0.2s rate=49816.2/s [progress] 11400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11400) elapsed=0.2s rate=49924.9/s [progress] 11500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11500) elapsed=0.2s rate=49615.9/s [progress] 11600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11600) elapsed=0.2s rate=49660.4/s [progress] 11700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11700) elapsed=0.2s rate=49671.0/s [progress] 11800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11800) elapsed=0.2s rate=49503.7/s [progress] 11900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=11900) elapsed=0.2s rate=49608.1/s [progress] 12000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12000) elapsed=0.2s rate=49720.0/s [progress] 12100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12100) elapsed=0.2s rate=49802.4/s [progress] 12200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12200) elapsed=0.2s rate=49886.5/s [progress] 12300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12300) elapsed=0.2s rate=49901.9/s [progress] 12400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12400) elapsed=0.2s rate=49736.4/s [progress] 12500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12500) elapsed=0.3s rate=49772.7/s [chrom] chr11 done in 0.0s [chrom] starting chr12 [progress] 12600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12600) elapsed=0.3s rate=49801.0/s [progress] 12700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12700) elapsed=0.3s rate=49834.3/s [progress] 12800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12800) elapsed=0.3s rate=49716.7/s [progress] 12900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=12900) elapsed=0.3s rate=49799.6/s [progress] 13000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13000) elapsed=0.3s rate=49870.6/s [progress] 13100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13100) elapsed=0.3s rate=49924.5/s [progress] 13200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13200) elapsed=0.3s rate=50016.4/s [progress] 13300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13300) elapsed=0.3s rate=49841.9/s [progress] 13400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13400) elapsed=0.3s rate=49907.0/s [progress] 13500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13500) elapsed=0.3s rate=49960.0/s [chrom] chr12 done in 0.0s [chrom] starting chr13 [progress] 13600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13600) elapsed=0.3s rate=50031.6/s [progress] 13700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13700) elapsed=0.3s rate=50056.9/s [progress] 13800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13800) elapsed=0.3s rate=49990.1/s [progress] 13900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=13900) elapsed=0.3s rate=50041.7/s [chrom] chr13 done in 0.0s [chrom] starting chr14 [progress] 14000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14000) elapsed=0.3s rate=50054.2/s [progress] 14100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14100) elapsed=0.3s rate=50084.0/s [progress] 14200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14200) elapsed=0.3s rate=50136.6/s [progress] 14300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14300) elapsed=0.3s rate=50037.5/s [progress] 14400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14400) elapsed=0.3s rate=50096.8/s [progress] 14500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14500) elapsed=0.3s rate=50188.6/s [progress] 14600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14600) elapsed=0.3s rate=50230.9/s [chrom] chr14 done in 0.0s [chrom] starting chr15 [progress] 14700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14700) elapsed=0.3s rate=50314.6/s [progress] 14800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14800) elapsed=0.3s rate=50349.2/s [progress] 14900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=14900) elapsed=0.3s rate=50216.8/s [progress] 15000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=15000) elapsed=0.3s rate=50216.9/s [progress] 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elapsed=0.3s rate=50330.4/s [progress] 16000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16000) elapsed=0.3s rate=50380.9/s [progress] 16100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16100) elapsed=0.3s rate=50426.1/s [progress] 16200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16200) elapsed=0.3s rate=50462.7/s [chrom] chr16 done in 0.0s [chrom] starting chr17 [progress] 16300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16300) elapsed=0.3s rate=50357.7/s [progress] 16400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16400) elapsed=0.3s rate=50418.3/s [progress] 16500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16500) elapsed=0.3s rate=50488.3/s [progress] 16600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16600) elapsed=0.3s rate=50560.2/s [progress] 16700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16700) elapsed=0.3s rate=50619.9/s [progress] 16800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16800) elapsed=0.3s rate=50652.3/s [progress] 16900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=16900) elapsed=0.3s rate=50589.9/s [progress] 17000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17000) elapsed=0.3s rate=50638.5/s [progress] 17100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17100) elapsed=0.3s rate=50639.2/s [progress] 17200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17200) elapsed=0.3s rate=50708.8/s [progress] 17300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17300) elapsed=0.3s rate=50772.2/s [progress] 17400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17400) elapsed=0.3s rate=50730.0/s [progress] 17500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17500) elapsed=0.3s rate=50768.5/s [progress] 17600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17600) elapsed=0.3s rate=50818.8/s [progress] 17700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17700) elapsed=0.3s rate=50870.7/s [progress] 17800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17800) elapsed=0.3s rate=50914.9/s [chrom] chr17 done in 0.0s [chrom] starting chr18 [progress] 17900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=17900) elapsed=0.4s rate=50966.9/s [progress] 18000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18000) elapsed=0.4s rate=50848.0/s [progress] 18100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18100) elapsed=0.4s rate=50898.1/s [chrom] chr18 done in 0.0s [chrom] starting chr19 [progress] 18200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18200) elapsed=0.4s rate=50885.2/s [progress] 18300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18300) elapsed=0.4s rate=50944.7/s [progress] 18400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18400) elapsed=0.4s rate=50985.0/s [progress] 18500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18500) elapsed=0.4s rate=50897.5/s [progress] 18600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18600) elapsed=0.4s rate=50914.8/s [progress] 18700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18700) elapsed=0.4s rate=50973.5/s [progress] 18800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18800) elapsed=0.4s rate=51052.5/s [progress] 18900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=18900) elapsed=0.4s rate=51096.5/s [progress] 19000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19000) elapsed=0.4s rate=51017.1/s [progress] 19100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19100) elapsed=0.4s rate=51069.2/s [progress] 19200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19200) elapsed=0.4s rate=51116.1/s [progress] 19300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19300) elapsed=0.4s rate=51153.9/s [progress] 19400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19400) elapsed=0.4s rate=51197.7/s [progress] 19500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19500) elapsed=0.4s rate=51231.1/s [progress] 19600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19600) elapsed=0.4s rate=51149.9/s [progress] 19700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19700) elapsed=0.4s rate=51201.3/s [progress] 19800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19800) elapsed=0.4s rate=51225.0/s [progress] 19900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=19900) elapsed=0.4s rate=51242.9/s [progress] 20000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20000) elapsed=0.4s rate=51271.6/s [progress] 20100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20100) elapsed=0.4s rate=51318.2/s [progress] 20200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20200) elapsed=0.4s rate=51247.0/s [progress] 20300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20300) elapsed=0.4s rate=51275.5/s [progress] 20400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20400) elapsed=0.4s rate=51327.7/s [progress] 20500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20500) elapsed=0.4s rate=51398.4/s [progress] 20600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20600) elapsed=0.4s rate=51424.3/s [progress] 20700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20700) elapsed=0.4s rate=51277.2/s [progress] 20800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20800) elapsed=0.4s rate=51317.5/s [progress] 20900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=20900) elapsed=0.4s rate=51378.4/s [progress] 21000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21000) elapsed=0.4s rate=51438.6/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=0.4s rate=51469.4/s [progress] 21200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21200) elapsed=0.4s rate=51295.6/s [progress] 21300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21300) elapsed=0.4s rate=51337.6/s [progress] 21400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21400) elapsed=0.4s rate=51383.8/s [progress] 21500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21500) elapsed=0.4s rate=51413.3/s [progress] 21600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21600) elapsed=0.4s rate=51452.8/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=0.4s rate=51465.9/s [progress] 21800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=21800) elapsed=0.4s rate=51399.9/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=0.4s rate=51424.8/s [progress] 22000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22000) elapsed=0.4s rate=51461.7/s [progress] 22100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22100) elapsed=0.4s rate=51496.9/s [progress] 22200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22200) elapsed=0.4s rate=51534.2/s [progress] 22300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22300) elapsed=0.4s rate=51534.5/s [progress] 22400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22400) elapsed=0.4s rate=51441.5/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=0.4s rate=51371.7/s [progress] 22600 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22600) elapsed=0.4s rate=51368.2/s [progress] 22700 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22700) elapsed=0.4s rate=51358.6/s [progress] 22800 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22800) elapsed=0.4s rate=51371.2/s [progress] 22900 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=22900) elapsed=0.4s rate=51418.0/s [progress] 23000 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23000) elapsed=0.4s rate=51437.3/s [progress] 23100 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23100) elapsed=0.4s rate=51467.8/s [progress] 23200 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23200) elapsed=0.5s rate=51500.7/s [progress] 23300 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23300) elapsed=0.5s rate=51484.8/s [progress] 23400 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23400) elapsed=0.5s rate=51515.3/s [progress] 23500 variants processed (ok=0 no_reads=0 ref_mismatch=0 other=23500) elapsed=0.5s rate=51550.3/s [chrom] chrX done in 0.0s [done] 23550 variants in 0.5s (ok=0 no_reads=0 ref_mismatch=0 other=23550)