Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/85ece627974e60e692c9021685a69e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/e1253e50a37a71b480151e4ed4d607/HG00136_x_HG00290_FF_5.mix.bam
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/targets/HG00136_x_HG00290_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/ee/e1253e50a37a71b480151e4ed4d607/HG00136_x_HG00290_FF_5.mix.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/85ece627974e60e692c9021685a69e/.command.run
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/vcfs/HG00136_x_HG00290_FF_5.vcf
==> STAGING COMPLETE (8 inputs)

[init] ff = 0.050
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG00136_x_HG00290_FF_5.mix.bam
[W::hts_idx_load3] The index file is older than the data file: HG00136_x_HG00290_FF_5.mix.bam.bai
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 23621 sites
[chrom] starting chr1
[progress] 100 variants processed (ok=100 no_reads=0 ref_mismatch=0 other=0) elapsed=30.8s rate=3.2/s
[progress] 200 variants processed (ok=200 no_reads=0 ref_mismatch=0 other=0) elapsed=53.4s rate=3.7/s
[progress] 300 variants processed (ok=300 no_reads=0 ref_mismatch=0 other=0) elapsed=85.8s rate=3.5/s
[progress] 400 variants processed (ok=400 no_reads=0 ref_mismatch=0 other=0) elapsed=118.6s rate=3.4/s
[progress] 500 variants processed (ok=500 no_reads=0 ref_mismatch=0 other=0) elapsed=143.9s rate=3.5/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=211.1s rate=3.3/s
[progress] 800 variants processed (ok=800 no_reads=0 ref_mismatch=0 other=0) elapsed=272.2s rate=2.9/s
[progress] 900 variants processed (ok=900 no_reads=0 ref_mismatch=0 other=0) elapsed=295.9s rate=3.0/s
[progress] 1000 variants processed (ok=1000 no_reads=0 ref_mismatch=0 other=0) elapsed=315.5s rate=3.2/s
[progress] 1100 variants processed (ok=1100 no_reads=0 ref_mismatch=0 other=0) elapsed=341.8s rate=3.2/s
[progress] 1200 variants processed (ok=1200 no_reads=0 ref_mismatch=0 other=0) elapsed=408.9s rate=2.9/s
[progress] 1300 variants processed (ok=1300 no_reads=0 ref_mismatch=0 other=0) elapsed=479.9s rate=2.7/s
[progress] 1400 variants processed (ok=1400 no_reads=0 ref_mismatch=0 other=0) elapsed=581.2s rate=2.4/s
[progress] 1500 variants processed (ok=1500 no_reads=0 ref_mismatch=0 other=0) elapsed=637.9s rate=2.4/s
[progress] 1600 variants processed (ok=1600 no_reads=0 ref_mismatch=0 other=0) elapsed=692.6s rate=2.3/s
[progress] 1700 variants processed (ok=1700 no_reads=0 ref_mismatch=0 other=0) elapsed=757.4s rate=2.2/s
[progress] 1800 variants processed (ok=1800 no_reads=0 ref_mismatch=0 other=0) elapsed=783.5s rate=2.3/s