Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/cf3698d8246dd02f473c79f1fe790a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/1cf98e3272290c8fa02b06eadf3a98/HG03540_x_HG03579_FF_5.mix.bam
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/targets/HG03540_x_HG03579_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/00/cf3698d8246dd02f473c79f1fe790a/.command.run
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/vcfs/HG03540_x_HG03579_FF_5.vcf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/1cf98e3272290c8fa02b06eadf3a98/HG03540_x_HG03579_FF_5.mix.bam.bai
==> STAGING COMPLETE (8 inputs)

[init] ff = 0.050
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG03540_x_HG03579_FF_5.mix.bam
[W::hts_idx_load3] The index file is older than the data file: HG03540_x_HG03579_FF_5.mix.bam.bai
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 43524 sites
[chrom] starting chr1
[progress] 100 variants processed (ok=100 no_reads=0 ref_mismatch=0 other=0) elapsed=24.2s rate=4.1/s
[progress] 200 variants processed (ok=200 no_reads=0 ref_mismatch=0 other=0) elapsed=43.9s rate=4.6/s
[progress] 300 variants processed (ok=300 no_reads=0 ref_mismatch=0 other=0) elapsed=60.6s rate=5.0/s
[progress] 400 variants processed (ok=400 no_reads=0 ref_mismatch=0 other=0) elapsed=76.9s rate=5.2/s
[progress] 500 variants processed (ok=500 no_reads=0 ref_mismatch=0 other=0) elapsed=96.0s rate=5.2/s
[progress] 600 variants processed (ok=600 no_reads=0 ref_mismatch=0 other=0) elapsed=122.6s rate=4.9/s
[progress] 700 variants processed (ok=700 no_reads=0 ref_mismatch=0 other=0) elapsed=143.6s rate=4.9/s
[progress] 800 variants processed (ok=800 no_reads=0 ref_mismatch=0 other=0) elapsed=161.6s rate=4.9/s
[progress] 900 variants processed (ok=900 no_reads=0 ref_mismatch=0 other=0) elapsed=180.9s rate=5.0/s
[progress] 1000 variants processed (ok=1000 no_reads=0 ref_mismatch=0 other=0) elapsed=203.2s rate=4.9/s
[progress] 1100 variants processed (ok=1100 no_reads=0 ref_mismatch=0 other=0) elapsed=223.4s rate=4.9/s
[progress] 1200 variants processed (ok=1200 no_reads=0 ref_mismatch=0 other=0) elapsed=241.1s rate=5.0/s
[progress] 1300 variants processed (ok=1300 no_reads=0 ref_mismatch=0 other=0) elapsed=260.6s rate=5.0/s
[progress] 1400 variants processed (ok=1400 no_reads=0 ref_mismatch=0 other=0) elapsed=288.0s rate=4.9/s
[progress] 1500 variants processed (ok=1500 no_reads=0 ref_mismatch=0 other=0) elapsed=305.4s rate=4.9/s
[progress] 1600 variants processed (ok=1600 no_reads=0 ref_mismatch=0 other=0) elapsed=333.7s rate=4.8/s
[progress] 1700 variants processed (ok=1700 no_reads=0 ref_mismatch=0 other=0) elapsed=353.7s rate=4.8/s
[progress] 1800 variants processed (ok=1800 no_reads=0 ref_mismatch=0 other=0) elapsed=375.6s rate=4.8/s
[progress] 1900 variants processed (ok=1900 no_reads=0 ref_mismatch=0 other=0) elapsed=391.8s rate=4.8/s
[progress] 2000 variants processed (ok=2000 no_reads=0 ref_mismatch=0 other=0) elapsed=409.1s rate=4.9/s
[progress] 2100 variants processed (ok=2100 no_reads=0 ref_mismatch=0 other=0) elapsed=423.5s rate=5.0/s
[progress] 2200 variants processed (ok=2200 no_reads=0 ref_mismatch=0 other=0) elapsed=441.8s rate=5.0/s
[progress] 2300 variants processed (ok=2300 no_reads=0 ref_mismatch=0 other=0) elapsed=460.0s rate=5.0/s
[progress] 2400 variants processed (ok=2400 no_reads=0 ref_mismatch=0 other=0) elapsed=482.1s rate=5.0/s
[progress] 2500 variants processed (ok=2500 no_reads=0 ref_mismatch=0 other=0) elapsed=501.7s rate=5.0/s
[progress] 2600 variants processed (ok=2600 no_reads=0 ref_mismatch=0 other=0) elapsed=530.4s rate=4.9/s
[progress] 2700 variants processed (ok=2700 no_reads=0 ref_mismatch=0 other=0) elapsed=584.5s rate=4.6/s
[progress] 2800 variants processed (ok=2800 no_reads=0 ref_mismatch=0 other=0) elapsed=635.1s rate=4.4/s
[progress] 2900 variants processed (ok=2900 no_reads=0 ref_mismatch=0 other=0) elapsed=672.1s rate=4.3/s
[progress] 3000 variants processed (ok=3000 no_reads=0 ref_mismatch=0 other=0) elapsed=716.8s rate=4.2/s
[progress] 3100 variants processed (ok=3100 no_reads=0 ref_mismatch=0 other=0) elapsed=736.7s rate=4.2/s
[progress] 3200 variants processed (ok=3200 no_reads=0 ref_mismatch=0 other=0) elapsed=757.9s rate=4.2/s