Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/5470cf6d41a3d6ab286533f0021548/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/786a2804e7f371871722930058fa5c/HG02855_x_HG02886_FF_10.mix.bam.bai
  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/HG02855_x_HG02886_FF_10.vcf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/786a2804e7f371871722930058fa5c/HG02855_x_HG02886_FF_10.mix.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/5470cf6d41a3d6ab286533f0021548/.command.run
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/targets/HG02855_x_HG02886_FF_10.targets.tsv
==> STAGING COMPLETE (8 inputs)

[init] ff = 0.100
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG02855_x_HG02886_FF_10.mix.bam
[W::hts_idx_load3] The index file is older than the data file: HG02855_x_HG02886_FF_10.mix.bam.bai
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 23548 sites
[chrom] starting chr1
[progress] 100 variants processed (ok=100 no_reads=0 ref_mismatch=0 other=0) elapsed=20.5s rate=4.9/s
[progress] 200 variants processed (ok=200 no_reads=0 ref_mismatch=0 other=0) elapsed=45.4s rate=4.4/s
[progress] 300 variants processed (ok=300 no_reads=0 ref_mismatch=0 other=0) elapsed=70.7s rate=4.2/s
[progress] 400 variants processed (ok=400 no_reads=0 ref_mismatch=0 other=0) elapsed=91.9s rate=4.4/s
[progress] 500 variants processed (ok=500 no_reads=0 ref_mismatch=0 other=0) elapsed=120.7s rate=4.1/s
[progress] 600 variants processed (ok=600 no_reads=0 ref_mismatch=0 other=0) elapsed=142.4s rate=4.2/s
[progress] 700 variants processed (ok=700 no_reads=0 ref_mismatch=0 other=0) elapsed=193.1s rate=3.6/s
[progress] 800 variants processed (ok=800 no_reads=0 ref_mismatch=0 other=0) elapsed=216.9s rate=3.7/s
[progress] 900 variants processed (ok=900 no_reads=0 ref_mismatch=0 other=0) elapsed=236.5s rate=3.8/s
[progress] 1000 variants processed (ok=1000 no_reads=0 ref_mismatch=0 other=0) elapsed=255.6s rate=3.9/s
[progress] 1100 variants processed (ok=1100 no_reads=0 ref_mismatch=0 other=0) elapsed=274.8s rate=4.0/s
[progress] 1200 variants processed (ok=1200 no_reads=0 ref_mismatch=0 other=0) elapsed=339.6s rate=3.5/s
[progress] 1300 variants processed (ok=1300 no_reads=0 ref_mismatch=0 other=0) elapsed=387.7s rate=3.4/s
[progress] 1400 variants processed (ok=1400 no_reads=0 ref_mismatch=0 other=0) elapsed=440.5s rate=3.2/s
[progress] 1500 variants processed (ok=1500 no_reads=0 ref_mismatch=0 other=0) elapsed=477.5s rate=3.1/s
[progress] 1600 variants processed (ok=1600 no_reads=0 ref_mismatch=0 other=0) elapsed=499.1s rate=3.2/s
[progress] 1700 variants processed (ok=1700 no_reads=0 ref_mismatch=0 other=0) elapsed=519.2s rate=3.3/s
[progress] 1800 variants processed (ok=1800 no_reads=0 ref_mismatch=0 other=0) elapsed=542.1s rate=3.3/s
[progress] 1900 variants processed (ok=1900 no_reads=0 ref_mismatch=0 other=0) elapsed=587.0s rate=3.2/s
[progress] 2000 variants processed (ok=2000 no_reads=0 ref_mismatch=0 other=0) elapsed=605.8s rate=3.3/s
[progress] 2100 variants processed (ok=2100 no_reads=0 ref_mismatch=0 other=0) elapsed=628.8s rate=3.3/s
[progress] 2200 variants processed (ok=2200 no_reads=0 ref_mismatch=0 other=0) elapsed=651.9s rate=3.4/s
[chrom] chr1 done in 672.3s
[chrom] starting chr2
[progress] 2300 variants processed (ok=2300 no_reads=0 ref_mismatch=0 other=0) elapsed=677.8s rate=3.4/s
[progress] 2400 variants processed (ok=2400 no_reads=0 ref_mismatch=0 other=0) elapsed=700.2s rate=3.4/s
[progress] 2500 variants processed (ok=2500 no_reads=0 ref_mismatch=0 other=0) elapsed=724.8s rate=3.4/s
[progress] 2600 variants processed (ok=2600 no_reads=0 ref_mismatch=0 other=0) elapsed=746.6s rate=3.5/s