Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/790edaead5baced6f7dea42fb69ef8/.command.sh
  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/HG00621_x_HG00673_FF_10.vcf
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/targets/HG00621_x_HG00673_FF_10.targets.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/d5ad815a70e6c1bb66f47c70af0f49/HG00621_x_HG00673_FF_10.mix.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/790edaead5baced6f7dea42fb69ef8/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/d5ad815a70e6c1bb66f47c70af0f49/HG00621_x_HG00673_FF_10.mix.bam
==> STAGING COMPLETE (8 inputs)

[init] ff = 0.100
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG00621_x_HG00673_FF_10.mix.bam
[W::hts_idx_load3] The index file is older than the data file: HG00621_x_HG00673_FF_10.mix.bam.bai
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 41676 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=41.2s rate=4.9/s
[progress] 300 variants processed (ok=300 no_reads=0 ref_mismatch=0 other=0) elapsed=62.5s rate=4.8/s
[progress] 400 variants processed (ok=400 no_reads=0 ref_mismatch=0 other=0) elapsed=83.4s rate=4.8/s
[progress] 500 variants processed (ok=500 no_reads=0 ref_mismatch=0 other=0) elapsed=106.3s rate=4.7/s
[progress] 600 variants processed (ok=600 no_reads=0 ref_mismatch=0 other=0) elapsed=127.6s rate=4.7/s
[progress] 700 variants processed (ok=700 no_reads=0 ref_mismatch=0 other=0) elapsed=148.9s rate=4.7/s
[progress] 800 variants processed (ok=800 no_reads=0 ref_mismatch=0 other=0) elapsed=168.3s rate=4.8/s
[progress] 900 variants processed (ok=900 no_reads=0 ref_mismatch=0 other=0) elapsed=193.6s rate=4.6/s
[progress] 1000 variants processed (ok=1000 no_reads=0 ref_mismatch=0 other=0) elapsed=214.1s rate=4.7/s
[progress] 1100 variants processed (ok=1100 no_reads=0 ref_mismatch=0 other=0) elapsed=235.5s rate=4.7/s
[progress] 1200 variants processed (ok=1200 no_reads=0 ref_mismatch=0 other=0) elapsed=255.1s rate=4.7/s
[progress] 1300 variants processed (ok=1300 no_reads=0 ref_mismatch=0 other=0) elapsed=279.2s rate=4.7/s
[progress] 1400 variants processed (ok=1400 no_reads=0 ref_mismatch=0 other=0) elapsed=315.2s rate=4.4/s
[progress] 1500 variants processed (ok=1500 no_reads=0 ref_mismatch=0 other=0) elapsed=333.1s rate=4.5/s
[progress] 1600 variants processed (ok=1600 no_reads=0 ref_mismatch=0 other=0) elapsed=352.0s rate=4.5/s
[progress] 1700 variants processed (ok=1700 no_reads=0 ref_mismatch=0 other=0) elapsed=368.9s rate=4.6/s
[progress] 1800 variants processed (ok=1800 no_reads=0 ref_mismatch=0 other=0) elapsed=385.3s rate=4.7/s
[progress] 1900 variants processed (ok=1900 no_reads=0 ref_mismatch=0 other=0) elapsed=403.7s rate=4.7/s
[progress] 2000 variants processed (ok=2000 no_reads=0 ref_mismatch=0 other=0) elapsed=421.6s rate=4.7/s
[progress] 2100 variants processed (ok=2100 no_reads=0 ref_mismatch=0 other=0) elapsed=442.8s rate=4.7/s
[progress] 2200 variants processed (ok=2200 no_reads=0 ref_mismatch=0 other=0) elapsed=459.0s rate=4.8/s
[progress] 2300 variants processed (ok=2300 no_reads=0 ref_mismatch=0 other=0) elapsed=480.4s rate=4.8/s
[progress] 2400 variants processed (ok=2400 no_reads=0 ref_mismatch=0 other=0) elapsed=501.3s rate=4.8/s
[progress] 2500 variants processed (ok=2500 no_reads=0 ref_mismatch=0 other=0) elapsed=547.5s rate=4.6/s
[progress] 2600 variants processed (ok=2600 no_reads=0 ref_mismatch=0 other=0) elapsed=614.8s rate=4.2/s
[progress] 2700 variants processed (ok=2700 no_reads=0 ref_mismatch=0 other=0) elapsed=654.1s rate=4.1/s
[progress] 2800 variants processed (ok=2800 no_reads=0 ref_mismatch=0 other=0) elapsed=705.3s rate=4.0/s
[progress] 2900 variants processed (ok=2900 no_reads=0 ref_mismatch=0 other=0) elapsed=729.8s rate=4.0/s
[progress] 3000 variants processed (ok=3000 no_reads=0 ref_mismatch=0 other=0) elapsed=751.8s rate=4.0/s
[progress] 3100 variants processed (ok=3100 no_reads=0 ref_mismatch=0 other=0) elapsed=772.2s rate=4.0/s
[progress] 3200 variants processed (ok=3200 no_reads=0 ref_mismatch=0 other=0) elapsed=793.2s rate=4.0/s