Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/cfeb7cfe5d86754de81bd11f08f08f/.command.sh
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/targets/HG02657_x_HG02682_FF_5.targets.tsv
  Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/vcfs/HG02657_x_HG02682_FF_5.vcf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/cfeb7cfe5d86754de81bd11f08f08f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/6459dcd5ba53de0788476a9edab6db/HG02657_x_HG02682_FF_5.mix.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/6459dcd5ba53de0788476a9edab6db/HG02657_x_HG02682_FF_5.mix.bam.bai
==> STAGING COMPLETE (8 inputs)

[init] ff = 0.050
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG02657_x_HG02682_FF_5.mix.bam
[W::hts_idx_load3] The index file is older than the data file: HG02657_x_HG02682_FF_5.mix.bam.bai
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 23098 sites
[chrom] starting chr1
[progress] 100 variants processed (ok=100 no_reads=0 ref_mismatch=0 other=0) elapsed=27.6s rate=3.6/s
[progress] 200 variants processed (ok=200 no_reads=0 ref_mismatch=0 other=0) elapsed=51.9s rate=3.9/s
[progress] 300 variants processed (ok=300 no_reads=0 ref_mismatch=0 other=0) elapsed=81.8s rate=3.7/s
[progress] 400 variants processed (ok=400 no_reads=0 ref_mismatch=0 other=0) elapsed=105.1s rate=3.8/s
[progress] 500 variants processed (ok=500 no_reads=0 ref_mismatch=0 other=0) elapsed=140.2s rate=3.6/s
[progress] 600 variants processed (ok=600 no_reads=0 ref_mismatch=0 other=0) elapsed=172.7s rate=3.5/s
[progress] 700 variants processed (ok=700 no_reads=0 ref_mismatch=0 other=0) elapsed=220.7s rate=3.2/s
[progress] 800 variants processed (ok=800 no_reads=0 ref_mismatch=0 other=0) elapsed=243.7s rate=3.3/s
[progress] 900 variants processed (ok=900 no_reads=0 ref_mismatch=0 other=0) elapsed=265.3s rate=3.4/s
[progress] 1000 variants processed (ok=1000 no_reads=0 ref_mismatch=0 other=0) elapsed=287.3s rate=3.5/s
[progress] 1100 variants processed (ok=1100 no_reads=0 ref_mismatch=0 other=0) elapsed=312.5s rate=3.5/s
[progress] 1200 variants processed (ok=1200 no_reads=0 ref_mismatch=0 other=0) elapsed=372.4s rate=3.2/s
[progress] 1300 variants processed (ok=1300 no_reads=0 ref_mismatch=0 other=0) elapsed=443.4s rate=2.9/s
[progress] 1400 variants processed (ok=1400 no_reads=0 ref_mismatch=0 other=0) elapsed=545.9s rate=2.6/s
[progress] 1500 variants processed (ok=1500 no_reads=0 ref_mismatch=0 other=0) elapsed=601.7s rate=2.5/s
[progress] 1600 variants processed (ok=1600 no_reads=0 ref_mismatch=0 other=0) elapsed=660.7s rate=2.4/s
[progress] 1700 variants processed (ok=1700 no_reads=0 ref_mismatch=0 other=0) elapsed=729.9s rate=2.3/s
[progress] 1800 variants processed (ok=1800 no_reads=0 ref_mismatch=0 other=0) elapsed=763.1s rate=2.4/s