Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/633cbbf00512e692b6c9ad9836692f/HG04098_x_HG04161_FF_10.mix.bam
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/vcfs/HG04098_x_HG04161_FF_10.vcf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/7c1bd882048bab064874ccedb257bc/.command.sh
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/targets/HG04098_x_HG04161_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/0a/633cbbf00512e692b6c9ad9836692f/HG04098_x_HG04161_FF_10.mix.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/7c1bd882048bab064874ccedb257bc/.command.run
==> STAGING COMPLETE (8 inputs)

[init] ff = 0.100
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG04098_x_HG04161_FF_10.mix.bam
[W::hts_idx_load3] The index file is older than the data file: HG04098_x_HG04161_FF_10.mix.bam.bai
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 18573 sites
[chrom] starting chr1
[progress] 100 variants processed (ok=100 no_reads=0 ref_mismatch=0 other=0) elapsed=24.6s rate=4.1/s
[progress] 200 variants processed (ok=200 no_reads=0 ref_mismatch=0 other=0) elapsed=48.7s rate=4.1/s