Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/a412858e111183448a27a9d9e738ce/HG00350_x_HG00438_FF_10.mix.bam.bai
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/targets/HG00350_x_HG00438_FF_10.targets.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/8634c34edb8bf463938c3fd9567318/.command.sh
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/vcfs/HG00350_x_HG00438_FF_10.vcf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/a412858e111183448a27a9d9e738ce/HG00350_x_HG00438_FF_10.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/9f/8634c34edb8bf463938c3fd9567318/.command.run
==> STAGING COMPLETE (8 inputs)

[init] ff = 0.100
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG00350_x_HG00438_FF_10.mix.bam
[W::hts_idx_load3] The index file is older than the data file: HG00350_x_HG00438_FF_10.mix.bam.bai
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 23740 sites
[chrom] starting chr1
[progress] 100 variants processed (ok=100 no_reads=0 ref_mismatch=0 other=0) elapsed=22.5s rate=4.4/s
[progress] 200 variants processed (ok=200 no_reads=0 ref_mismatch=0 other=0) elapsed=41.2s rate=4.9/s
[progress] 300 variants processed (ok=300 no_reads=0 ref_mismatch=0 other=0) elapsed=63.7s rate=4.7/s
[progress] 400 variants processed (ok=400 no_reads=0 ref_mismatch=0 other=0) elapsed=87.7s rate=4.6/s
[progress] 500 variants processed (ok=500 no_reads=0 ref_mismatch=0 other=0) elapsed=109.5s rate=4.6/s
[progress] 600 variants processed (ok=600 no_reads=0 ref_mismatch=0 other=0) elapsed=129.4s rate=4.6/s
[progress] 700 variants processed (ok=700 no_reads=0 ref_mismatch=0 other=0) elapsed=156.5s rate=4.5/s
[progress] 800 variants processed (ok=800 no_reads=0 ref_mismatch=0 other=0) elapsed=186.0s rate=4.3/s
[progress] 900 variants processed (ok=900 no_reads=0 ref_mismatch=0 other=0) elapsed=204.0s rate=4.4/s
[progress] 1000 variants processed (ok=1000 no_reads=0 ref_mismatch=0 other=0) elapsed=219.0s rate=4.6/s
[progress] 1100 variants processed (ok=1100 no_reads=0 ref_mismatch=0 other=0) elapsed=237.8s rate=4.6/s
[progress] 1200 variants processed (ok=1200 no_reads=0 ref_mismatch=0 other=0) elapsed=257.3s rate=4.7/s
[progress] 1300 variants processed (ok=1300 no_reads=0 ref_mismatch=0 other=0) elapsed=277.9s rate=4.7/s
[progress] 1400 variants processed (ok=1400 no_reads=0 ref_mismatch=0 other=0) elapsed=325.2s rate=4.3/s
[progress] 1500 variants processed (ok=1500 no_reads=0 ref_mismatch=0 other=0) elapsed=374.4s rate=4.0/s
[progress] 1600 variants processed (ok=1600 no_reads=0 ref_mismatch=0 other=0) elapsed=418.7s rate=3.8/s
[progress] 1700 variants processed (ok=1700 no_reads=0 ref_mismatch=0 other=0) elapsed=443.3s rate=3.8/s
[progress] 1800 variants processed (ok=1800 no_reads=0 ref_mismatch=0 other=0) elapsed=462.8s rate=3.9/s
[progress] 1900 variants processed (ok=1900 no_reads=0 ref_mismatch=0 other=0) elapsed=482.4s rate=3.9/s
[progress] 2000 variants processed (ok=2000 no_reads=0 ref_mismatch=0 other=0) elapsed=511.6s rate=3.9/s
[progress] 2100 variants processed (ok=2100 no_reads=0 ref_mismatch=0 other=0) elapsed=533.9s rate=3.9/s
[progress] 2200 variants processed (ok=2200 no_reads=0 ref_mismatch=0 other=0) elapsed=551.7s rate=4.0/s
[progress] 2300 variants processed (ok=2300 no_reads=0 ref_mismatch=0 other=0) elapsed=570.6s rate=4.0/s
[progress] 2400 variants processed (ok=2400 no_reads=0 ref_mismatch=0 other=0) elapsed=591.4s rate=4.1/s
[chrom] chr1 done in 604.0s
[chrom] starting chr2
[progress] 2500 variants processed (ok=2500 no_reads=0 ref_mismatch=0 other=0) elapsed=613.8s rate=4.1/s
[progress] 2600 variants processed (ok=2600 no_reads=0 ref_mismatch=0 other=0) elapsed=633.1s rate=4.1/s
[progress] 2700 variants processed (ok=2700 no_reads=0 ref_mismatch=0 other=0) elapsed=655.7s rate=4.1/s
[progress] 2800 variants processed (ok=2800 no_reads=0 ref_mismatch=0 other=0) elapsed=676.1s rate=4.1/s
[progress] 2900 variants processed (ok=2900 no_reads=0 ref_mismatch=0 other=0) elapsed=699.8s rate=4.1/s
[progress] 3000 variants processed (ok=3000 no_reads=0 ref_mismatch=0 other=0) elapsed=722.9s rate=4.2/s
[progress] 3100 variants processed (ok=3100 no_reads=0 ref_mismatch=0 other=0) elapsed=742.0s rate=4.2/s
[progress] 3200 variants processed (ok=3200 no_reads=0 ref_mismatch=0 other=0) elapsed=760.1s rate=4.2/s