Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/7ac91a90efc180b78838ad3a919c6a/.command.sh
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/vcfs/HG02622_x_HG02630_FF_5.vcf
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/targets/HG02622_x_HG02630_FF_5.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/2a/7ac91a90efc180b78838ad3a919c6a/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/e938bd8d1ba18a7ef31eea9144795c/HG02622_x_HG02630_FF_5.mix.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/e938bd8d1ba18a7ef31eea9144795c/HG02622_x_HG02630_FF_5.mix.bam.bai
==> STAGING COMPLETE (8 inputs)

[init] ff = 0.050
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG02622_x_HG02630_FF_5.mix.bam
[W::hts_idx_load3] The index file is older than the data file: HG02622_x_HG02630_FF_5.mix.bam.bai
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 30156 sites
[chrom] starting chr1
[progress] 100 variants processed (ok=100 no_reads=0 ref_mismatch=0 other=0) elapsed=28.7s rate=3.5/s
[progress] 200 variants processed (ok=200 no_reads=0 ref_mismatch=0 other=0) elapsed=48.9s rate=4.1/s
[progress] 300 variants processed (ok=300 no_reads=0 ref_mismatch=0 other=0) elapsed=72.7s rate=4.1/s
[progress] 400 variants processed (ok=400 no_reads=0 ref_mismatch=0 other=0) elapsed=99.0s rate=4.0/s