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/targets/HG01868_x_HG01891_FF_10.targets.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/e8b0a27fe7b4c3f32e054f93c85f62/.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/e9/70be221f5ebd53b87d9ab6c12d43aa/HG01868_x_HG01891_FF_10.mix.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/e8b0a27fe7b4c3f32e054f93c85f62/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/70be221f5ebd53b87d9ab6c12d43aa/HG01868_x_HG01891_FF_10.mix.bam.bai
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/vcfs/HG01868_x_HG01891_FF_10.vcf
==> STAGING COMPLETE (8 inputs)

[init] ff = 0.100
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG01868_x_HG01891_FF_10.mix.bam
[W::hts_idx_load3] The index file is older than the data file: HG01868_x_HG01891_FF_10.mix.bam.bai
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 17552 sites
[chrom] starting chr1
[progress] 100 variants processed (ok=100 no_reads=0 ref_mismatch=0 other=0) elapsed=28.0s rate=3.6/s
[progress] 200 variants processed (ok=200 no_reads=0 ref_mismatch=0 other=0) elapsed=49.8s rate=4.0/s
[progress] 300 variants processed (ok=300 no_reads=0 ref_mismatch=0 other=0) elapsed=79.1s rate=3.8/s
[progress] 400 variants processed (ok=400 no_reads=0 ref_mismatch=0 other=0) elapsed=102.8s rate=3.9/s
[progress] 500 variants processed (ok=500 no_reads=0 ref_mismatch=0 other=0) elapsed=140.4s rate=3.6/s
[progress] 600 variants processed (ok=600 no_reads=0 ref_mismatch=0 other=0) elapsed=166.9s rate=3.6/s
[progress] 700 variants processed (ok=700 no_reads=0 ref_mismatch=0 other=0) elapsed=186.8s rate=3.7/s
[progress] 800 variants processed (ok=800 no_reads=0 ref_mismatch=0 other=0) elapsed=207.3s rate=3.9/s
[progress] 900 variants processed (ok=900 no_reads=0 ref_mismatch=0 other=0) elapsed=272.6s rate=3.3/s
[progress] 1000 variants processed (ok=1000 no_reads=0 ref_mismatch=0 other=0) elapsed=332.8s rate=3.0/s
[progress] 1100 variants processed (ok=1100 no_reads=0 ref_mismatch=0 other=0) elapsed=391.2s rate=2.8/s
[progress] 1200 variants processed (ok=1200 no_reads=0 ref_mismatch=0 other=0) elapsed=428.2s rate=2.8/s
[progress] 1300 variants processed (ok=1300 no_reads=0 ref_mismatch=0 other=0) elapsed=449.8s rate=2.9/s
[progress] 1400 variants processed (ok=1400 no_reads=0 ref_mismatch=0 other=0) elapsed=493.1s rate=2.8/s
[progress] 1500 variants processed (ok=1500 no_reads=0 ref_mismatch=0 other=0) elapsed=524.8s rate=2.9/s
[progress] 1600 variants processed (ok=1600 no_reads=0 ref_mismatch=0 other=0) elapsed=545.1s rate=2.9/s
[progress] 1700 variants processed (ok=1700 no_reads=0 ref_mismatch=0 other=0) elapsed=567.7s rate=3.0/s
[chrom] chr1 done in 578.8s
[chrom] starting chr2
[progress] 1800 variants processed (ok=1800 no_reads=0 ref_mismatch=0 other=0) elapsed=591.7s rate=3.0/s
[progress] 1900 variants processed (ok=1900 no_reads=0 ref_mismatch=0 other=0) elapsed=618.3s rate=3.1/s
[progress] 2000 variants processed (ok=2000 no_reads=0 ref_mismatch=0 other=0) elapsed=644.2s rate=3.1/s
[progress] 2100 variants processed (ok=2100 no_reads=0 ref_mismatch=0 other=0) elapsed=668.5s rate=3.1/s
[progress] 2200 variants processed (ok=2200 no_reads=0 ref_mismatch=0 other=0) elapsed=688.6s rate=3.2/s
[progress] 2300 variants processed (ok=2300 no_reads=0 ref_mismatch=0 other=0) elapsed=712.4s rate=3.2/s
[progress] 2400 variants processed (ok=2400 no_reads=0 ref_mismatch=0 other=0) elapsed=740.5s rate=3.2/s
[progress] 2500 variants processed (ok=2500 no_reads=0 ref_mismatch=0 other=0) elapsed=761.9s rate=3.3/s