Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/5978058d18c882f2e032179802d943/.command.sh
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/vcfs/HG01928_x_HG01952_FF_5.vcf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/465b92a430ca73ae351071557e851b/HG01928_x_HG01952_FF_5.mix.bam
  Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/5978058d18c882f2e032179802d943/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/465b92a430ca73ae351071557e851b/HG01928_x_HG01952_FF_5.mix.bam.bai
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/targets/HG01928_x_HG01952_FF_5.targets.tsv
==> STAGING COMPLETE (8 inputs)

[init] ff = 0.050
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG01928_x_HG01952_FF_5.mix.bam
[W::hts_idx_load3] The index file is older than the data file: HG01928_x_HG01952_FF_5.mix.bam.bai
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 41869 sites
[chrom] starting chr1
[progress] 100 variants processed (ok=100 no_reads=0 ref_mismatch=0 other=0) elapsed=26.5s rate=3.8/s
[progress] 200 variants processed (ok=200 no_reads=0 ref_mismatch=0 other=0) elapsed=46.9s rate=4.3/s
[progress] 300 variants processed (ok=300 no_reads=0 ref_mismatch=0 other=0) elapsed=66.1s rate=4.5/s
[progress] 400 variants processed (ok=400 no_reads=0 ref_mismatch=0 other=0) elapsed=84.3s rate=4.7/s
[progress] 500 variants processed (ok=500 no_reads=0 ref_mismatch=0 other=0) elapsed=106.2s rate=4.7/s
[progress] 600 variants processed (ok=600 no_reads=0 ref_mismatch=0 other=0) elapsed=136.4s rate=4.4/s
[progress] 700 variants processed (ok=700 no_reads=0 ref_mismatch=0 other=0) elapsed=156.6s rate=4.5/s
[progress] 800 variants processed (ok=800 no_reads=0 ref_mismatch=0 other=0) elapsed=175.1s rate=4.6/s
[progress] 900 variants processed (ok=900 no_reads=0 ref_mismatch=0 other=0) elapsed=195.1s rate=4.6/s
[progress] 1000 variants processed (ok=1000 no_reads=0 ref_mismatch=0 other=0) elapsed=219.3s rate=4.6/s
[progress] 1100 variants processed (ok=1100 no_reads=0 ref_mismatch=0 other=0) elapsed=236.3s rate=4.7/s
[progress] 1200 variants processed (ok=1200 no_reads=0 ref_mismatch=0 other=0) elapsed=257.8s rate=4.7/s
[progress] 1300 variants processed (ok=1300 no_reads=0 ref_mismatch=0 other=0) elapsed=283.7s rate=4.6/s
[progress] 1400 variants processed (ok=1400 no_reads=0 ref_mismatch=0 other=0) elapsed=300.9s rate=4.7/s
[progress] 1500 variants processed (ok=1500 no_reads=0 ref_mismatch=0 other=0) elapsed=320.3s rate=4.7/s
[progress] 1600 variants processed (ok=1600 no_reads=0 ref_mismatch=0 other=0) elapsed=359.2s rate=4.5/s
[progress] 1700 variants processed (ok=1700 no_reads=0 ref_mismatch=0 other=0) elapsed=379.3s rate=4.5/s
[progress] 1800 variants processed (ok=1800 no_reads=0 ref_mismatch=0 other=0) elapsed=396.7s rate=4.5/s
[progress] 1900 variants processed (ok=1900 no_reads=0 ref_mismatch=0 other=0) elapsed=414.2s rate=4.6/s
[progress] 2000 variants processed (ok=2000 no_reads=0 ref_mismatch=0 other=0) elapsed=434.3s rate=4.6/s
[progress] 2100 variants processed (ok=2100 no_reads=0 ref_mismatch=0 other=0) elapsed=451.4s rate=4.7/s
[progress] 2200 variants processed (ok=2200 no_reads=0 ref_mismatch=0 other=0) elapsed=473.5s rate=4.6/s
[progress] 2300 variants processed (ok=2300 no_reads=0 ref_mismatch=0 other=0) elapsed=494.2s rate=4.7/s
[progress] 2400 variants processed (ok=2400 no_reads=0 ref_mismatch=0 other=0) elapsed=513.0s rate=4.7/s
[progress] 2500 variants processed (ok=2500 no_reads=0 ref_mismatch=0 other=0) elapsed=534.0s rate=4.7/s
[progress] 2600 variants processed (ok=2600 no_reads=0 ref_mismatch=0 other=0) elapsed=593.8s rate=4.4/s
[progress] 2700 variants processed (ok=2700 no_reads=0 ref_mismatch=0 other=0) elapsed=637.3s rate=4.2/s
[progress] 2800 variants processed (ok=2800 no_reads=0 ref_mismatch=0 other=0) elapsed=677.2s rate=4.1/s
[progress] 2900 variants processed (ok=2900 no_reads=0 ref_mismatch=0 other=0) elapsed=720.0s rate=4.0/s
[progress] 3000 variants processed (ok=3000 no_reads=0 ref_mismatch=0 other=0) elapsed=744.1s rate=4.0/s
[progress] 3100 variants processed (ok=3100 no_reads=0 ref_mismatch=0 other=0) elapsed=767.0s rate=4.0/s
[progress] 3200 variants processed (ok=3200 no_reads=0 ref_mismatch=0 other=0) elapsed=787.0s rate=4.1/s