Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/23ca4286e3682d945b29e7df5a273b/HG01361_x_HG01503_FF_5.mix.bam.bai
  Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/targets/HG01361_x_HG01503_FF_5.targets.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/afe3c1f64f2222e6acb79c08f0481f/.command.sh
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/vcfs/HG01361_x_HG01503_FF_5.vcf
  Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/afe3c1f64f2222e6acb79c08f0481f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/23ca4286e3682d945b29e7df5a273b/HG01361_x_HG01503_FF_5.mix.bam
==> STAGING COMPLETE (8 inputs)

[init] ff = 0.050
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG01361_x_HG01503_FF_5.mix.bam
[W::hts_idx_load3] The index file is older than the data file: HG01361_x_HG01503_FF_5.mix.bam.bai
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 636 sites
[chrom] starting chr1
[chrom] chr1 done in 15.8s
[chrom] starting chr2
[chrom] chr2 done in 7.2s
[chrom] starting chr3
[progress] 100 variants processed (ok=100 no_reads=0 ref_mismatch=0 other=0) elapsed=23.6s rate=4.2/s
[chrom] chr3 done in 8.2s
[chrom] starting chr4
[chrom] chr4 done in 8.1s
[chrom] starting chr5
[chrom] chr5 done in 5.7s
[chrom] starting chr6
[progress] 200 variants processed (ok=200 no_reads=0 ref_mismatch=0 other=0) elapsed=51.3s rate=3.9/s
[chrom] chr6 done in 9.1s
[chrom] starting chr7
[chrom] chr7 done in 7.5s
[chrom] starting chr8
[chrom] chr8 done in 3.3s
[chrom] starting chr9
[chrom] chr9 done in 9.1s
[chrom] starting chr10
[progress] 300 variants processed (ok=300 no_reads=0 ref_mismatch=0 other=0) elapsed=75.8s rate=4.0/s
[chrom] chr10 done in 3.4s
[chrom] starting chr11
[chrom] chr11 done in 13.3s
[chrom] starting chr12
[chrom] chr12 done in 10.8s
[chrom] starting chr13
[progress] 400 variants processed (ok=400 no_reads=0 ref_mismatch=0 other=0) elapsed=102.2s rate=3.9/s
[chrom] chr13 done in 2.3s
[chrom] starting chr14
[chrom] chr14 done in 6.3s
[chrom] starting chr15
[chrom] chr15 done in 7.0s
[chrom] starting chr16
[chrom] chr16 done in 6.7s
[chrom] starting chr17
[progress] 500 variants processed (ok=500 no_reads=0 ref_mismatch=0 other=0) elapsed=128.4s rate=3.9/s
[chrom] chr17 done in 13.5s
[chrom] starting chr18
[chrom] chr18 done in 1.8s
[chrom] starting chr19
[chrom] chr19 done in 13.3s
[chrom] starting chr20
[progress] 600 variants processed (ok=600 no_reads=0 ref_mismatch=0 other=0) elapsed=153.6s rate=3.9/s
[chrom] chr20 done in 3.9s
[chrom] starting chr21
[chrom] chr21 done in 3.3s
[chrom] starting chr22
[chrom] chr22 done in 3.9s
[done] 638 variants in 163.3s (ok=638 no_reads=0 ref_mismatch=0 other=0)