Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/700cfd56144c8ac6213c7786eeabdd/.command.sh
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/vcfs/HG01109_x_HG01175_FF_5.vcf
  Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/2d3803f2319687369aeafa77ec09f2/HG01109_x_HG01175_FF_5.mix.bam
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/targets/HG01109_x_HG01175_FF_5.targets.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/700cfd56144c8ac6213c7786eeabdd/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/2d3803f2319687369aeafa77ec09f2/HG01109_x_HG01175_FF_5.mix.bam.bai
==> STAGING COMPLETE (8 inputs)

[init] ff = 0.050
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG01109_x_HG01175_FF_5.mix.bam
[W::hts_idx_load3] The index file is older than the data file: HG01109_x_HG01175_FF_5.mix.bam.bai
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 28468 sites
[chrom] starting chr1
[progress] 100 variants processed (ok=100 no_reads=0 ref_mismatch=0 other=0) elapsed=26.7s rate=3.8/s
[progress] 200 variants processed (ok=200 no_reads=0 ref_mismatch=0 other=0) elapsed=47.7s rate=4.2/s
[progress] 300 variants processed (ok=300 no_reads=0 ref_mismatch=0 other=0) elapsed=76.7s rate=3.9/s
[progress] 400 variants processed (ok=400 no_reads=0 ref_mismatch=0 other=0) elapsed=99.0s rate=4.0/s
[progress] 500 variants processed (ok=500 no_reads=0 ref_mismatch=0 other=0) elapsed=130.8s rate=3.8/s
[progress] 600 variants processed (ok=600 no_reads=0 ref_mismatch=0 other=0) elapsed=156.2s rate=3.8/s
[progress] 700 variants processed (ok=700 no_reads=0 ref_mismatch=0 other=0) elapsed=187.9s rate=3.7/s
[progress] 800 variants processed (ok=800 no_reads=0 ref_mismatch=0 other=0) elapsed=255.9s rate=3.1/s
[progress] 900 variants processed (ok=900 no_reads=0 ref_mismatch=0 other=0) elapsed=278.9s rate=3.2/s
[progress] 1000 variants processed (ok=1000 no_reads=0 ref_mismatch=0 other=0) elapsed=300.2s rate=3.3/s
[progress] 1100 variants processed (ok=1100 no_reads=0 ref_mismatch=0 other=0) elapsed=322.0s rate=3.4/s
[progress] 1200 variants processed (ok=1200 no_reads=0 ref_mismatch=0 other=0) elapsed=344.1s rate=3.5/s
[progress] 1300 variants processed (ok=1300 no_reads=0 ref_mismatch=0 other=0) elapsed=368.5s rate=3.5/s
[progress] 1400 variants processed (ok=1400 no_reads=0 ref_mismatch=0 other=0) elapsed=392.1s rate=3.6/s
[progress] 1500 variants processed (ok=1500 no_reads=0 ref_mismatch=0 other=0) elapsed=461.7s rate=3.2/s
[progress] 1600 variants processed (ok=1600 no_reads=0 ref_mismatch=0 other=0) elapsed=523.1s rate=3.1/s
[progress] 1700 variants processed (ok=1700 no_reads=0 ref_mismatch=0 other=0) elapsed=577.8s rate=2.9/s
[progress] 1800 variants processed (ok=1800 no_reads=0 ref_mismatch=0 other=0) elapsed=639.2s rate=2.8/s
[progress] 1900 variants processed (ok=1900 no_reads=0 ref_mismatch=0 other=0) elapsed=698.4s rate=2.7/s
[progress] 2000 variants processed (ok=2000 no_reads=0 ref_mismatch=0 other=0) elapsed=728.4s rate=2.7/s
[progress] 2100 variants processed (ok=2100 no_reads=0 ref_mismatch=0 other=0) elapsed=754.9s rate=2.8/s
[progress] 2200 variants processed (ok=2200 no_reads=0 ref_mismatch=0 other=0) elapsed=777.3s rate=2.8/s