Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/4ca1b4a5746d63935eac3a046ab043/.command.sh
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/targets/HG03492_x_HG03516_FF_10.targets.tsv
  Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/4ca1b4a5746d63935eac3a046ab043/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/0f6ccecb7d14e5e27edab8c235da02/HG03492_x_HG03516_FF_10.mix.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/0f6ccecb7d14e5e27edab8c235da02/HG03492_x_HG03516_FF_10.mix.bam
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/vcfs/HG03492_x_HG03516_FF_10.vcf
==> STAGING COMPLETE (8 inputs)

[init] ff = 0.100
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG03492_x_HG03516_FF_10.mix.bam
[W::hts_idx_load3] The index file is older than the data file: HG03492_x_HG03516_FF_10.mix.bam.bai
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 21723 sites
[chrom] starting chr1
[progress] 100 variants processed (ok=100 no_reads=0 ref_mismatch=0 other=0) elapsed=26.7s rate=3.7/s
[progress] 200 variants processed (ok=200 no_reads=0 ref_mismatch=0 other=0) elapsed=51.7s rate=3.9/s
[progress] 300 variants processed (ok=300 no_reads=0 ref_mismatch=0 other=0) elapsed=79.3s rate=3.8/s