Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/f832395cfb28f10c857aa94c524fc1/.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/13/0217ad21d9050074fdfdd774b04422/HG01956_x_HG01978_FF_5.mix.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/f832395cfb28f10c857aa94c524fc1/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/0217ad21d9050074fdfdd774b04422/HG01956_x_HG01978_FF_5.mix.bam
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/vcfs/HG01956_x_HG01978_FF_5.vcf
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/targets/HG01956_x_HG01978_FF_5.targets.tsv
==> STAGING COMPLETE (8 inputs)

[init] ff = 0.050
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG01956_x_HG01978_FF_5.mix.bam
[W::hts_idx_load3] The index file is older than the data file: HG01956_x_HG01978_FF_5.mix.bam.bai
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 23632 sites
[chrom] starting chr1
[progress] 100 variants processed (ok=100 no_reads=0 ref_mismatch=0 other=0) elapsed=26.4s rate=3.8/s
[progress] 200 variants processed (ok=200 no_reads=0 ref_mismatch=0 other=0) elapsed=47.1s rate=4.2/s
[progress] 300 variants processed (ok=300 no_reads=0 ref_mismatch=0 other=0) elapsed=75.1s rate=4.0/s
[progress] 400 variants processed (ok=400 no_reads=0 ref_mismatch=0 other=0) elapsed=102.4s rate=3.9/s