Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/28dc2391a408a2e48940fbeb95ef9b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/b5d7bce709b3a6733db0f62e45cd1e/HG02657_x_HG02682_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/5a/b5d7bce709b3a6733db0f62e45cd1e/HG02657_x_HG02682_FF_10.mix.bam.bai
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/vcfs/HG02657_x_HG02682_FF_10.vcf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/28dc2391a408a2e48940fbeb95ef9b/.command.run
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/targets/HG02657_x_HG02682_FF_10.targets.tsv
==> STAGING COMPLETE (8 inputs)

[init] ff = 0.100
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG02657_x_HG02682_FF_10.mix.bam
[W::hts_idx_load3] The index file is older than the data file: HG02657_x_HG02682_FF_10.mix.bam.bai
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 18084 sites
[chrom] starting chr1
[progress] 100 variants processed (ok=100 no_reads=0 ref_mismatch=0 other=0) elapsed=25.2s rate=4.0/s
[progress] 200 variants processed (ok=200 no_reads=0 ref_mismatch=0 other=0) elapsed=51.3s rate=3.9/s
[progress] 300 variants processed (ok=300 no_reads=0 ref_mismatch=0 other=0) elapsed=73.8s rate=4.1/s
[progress] 400 variants processed (ok=400 no_reads=0 ref_mismatch=0 other=0) elapsed=109.0s rate=3.7/s
[progress] 500 variants processed (ok=500 no_reads=0 ref_mismatch=0 other=0) elapsed=138.4s rate=3.6/s
[progress] 600 variants processed (ok=600 no_reads=0 ref_mismatch=0 other=0) elapsed=179.3s rate=3.3/s
[progress] 700 variants processed (ok=700 no_reads=0 ref_mismatch=0 other=0) elapsed=200.2s rate=3.5/s
[progress] 800 variants processed (ok=800 no_reads=0 ref_mismatch=0 other=0) elapsed=222.6s rate=3.6/s
[progress] 900 variants processed (ok=900 no_reads=0 ref_mismatch=0 other=0) elapsed=260.8s rate=3.5/s
[progress] 1000 variants processed (ok=1000 no_reads=0 ref_mismatch=0 other=0) elapsed=328.3s rate=3.0/s
[progress] 1100 variants processed (ok=1100 no_reads=0 ref_mismatch=0 other=0) elapsed=419.5s rate=2.6/s
[progress] 1200 variants processed (ok=1200 no_reads=0 ref_mismatch=0 other=0) elapsed=472.3s rate=2.5/s
[progress] 1300 variants processed (ok=1300 no_reads=0 ref_mismatch=0 other=0) elapsed=533.1s rate=2.4/s
[progress] 1400 variants processed (ok=1400 no_reads=0 ref_mismatch=0 other=0) elapsed=561.6s rate=2.5/s
[progress] 1500 variants processed (ok=1500 no_reads=0 ref_mismatch=0 other=0) elapsed=586.7s rate=2.6/s
[progress] 1600 variants processed (ok=1600 no_reads=0 ref_mismatch=0 other=0) elapsed=637.4s rate=2.5/s
[progress] 1700 variants processed (ok=1700 no_reads=0 ref_mismatch=0 other=0) elapsed=660.4s rate=2.6/s
[progress] 1800 variants processed (ok=1800 no_reads=0 ref_mismatch=0 other=0) elapsed=684.3s rate=2.6/s
[chrom] chr1 done in 704.5s
[chrom] starting chr2
[progress] 1900 variants processed (ok=1900 no_reads=0 ref_mismatch=0 other=0) elapsed=710.4s rate=2.7/s
[progress] 2000 variants processed (ok=2000 no_reads=0 ref_mismatch=0 other=0) elapsed=736.1s rate=2.7/s
[progress] 2100 variants processed (ok=2100 no_reads=0 ref_mismatch=0 other=0) elapsed=758.9s rate=2.8/s