Downloading: s3://natera-platform-sandbox/users/sgoyal/resources/GRCh38/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/38995d1b2cd57a23ed911eafbc13e3/.command.sh
  Downloading: s3://natera-platform-sandbox/users/tdouglas/nipt_caller/adaptive_alpha_features/inputs/targets/HG02657_x_HG02682_FF_5.targets.tsv
  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/HG02657_x_HG02682_FF_5.vcf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/38995d1b2cd57a23ed911eafbc13e3/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/6459dcd5ba53de0788476a9edab6db/HG02657_x_HG02682_FF_5.mix.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/6459dcd5ba53de0788476a9edab6db/HG02657_x_HG02682_FF_5.mix.bam.bai
==> STAGING COMPLETE (8 inputs)

[init] ff = 0.050
[init] alphas = [0.012, 0.05, 0.1]
[init] opening BAM HG02657_x_HG02682_FF_5.mix.bam
[W::hts_idx_load3] The index file is older than the data file: HG02657_x_HG02682_FF_5.mix.bam.bai
[init] opening reference Homo_sapiens_assembly38.fasta
[init] target list: 642 sites
[chrom] starting chr1
[chrom] chr1 done in 13.5s
[chrom] starting chr2
[chrom] chr2 done in 7.8s
[chrom] starting chr3
[progress] 100 variants processed (ok=100 no_reads=0 ref_mismatch=0 other=0) elapsed=23.3s rate=4.3/s
[chrom] chr3 done in 8.8s
[chrom] starting chr4
[chrom] chr4 done in 10.5s
[chrom] starting chr5
[chrom] chr5 done in 6.0s
[chrom] starting chr6
[progress] 200 variants processed (ok=200 no_reads=0 ref_mismatch=0 other=0) elapsed=50.8s rate=3.9/s
[chrom] chr6 done in 9.4s
[chrom] starting chr7
[chrom] chr7 done in 7.5s
[chrom] starting chr8
[chrom] chr8 done in 3.9s
[chrom] starting chr9
[progress] 300 variants processed (ok=300 no_reads=0 ref_mismatch=0 other=0) elapsed=73.4s rate=4.1/s
[chrom] chr9 done in 6.6s
[chrom] starting chr10
[chrom] chr10 done in 4.1s
[chrom] starting chr11
[chrom] chr11 done in 9.4s
[chrom] starting chr12
[chrom] chr12 done in 9.2s
[chrom] starting chr13
[progress] 400 variants processed (ok=400 no_reads=0 ref_mismatch=0 other=0) elapsed=97.9s rate=4.1/s
[chrom] chr13 done in 2.8s
[chrom] starting chr14
[chrom] chr14 done in 5.2s
[chrom] starting chr15
[chrom] chr15 done in 4.2s
[chrom] starting chr16
[chrom] chr16 done in 5.5s
[chrom] starting chr17
[progress] 500 variants processed (ok=500 no_reads=0 ref_mismatch=0 other=0) elapsed=120.8s rate=4.1/s
[chrom] chr17 done in 16.4s
[chrom] starting chr18
[chrom] chr18 done in 1.8s
[chrom] starting chr19
[progress] 600 variants processed (ok=600 no_reads=0 ref_mismatch=0 other=0) elapsed=146.9s rate=4.1/s
[chrom] chr19 done in 14.3s
[chrom] starting chr20
[chrom] chr20 done in 3.4s
[chrom] starting chr21
[chrom] chr21 done in 4.3s
[chrom] starting chr22
[chrom] chr22 done in 2.7s
[done] 644 variants in 157.3s (ok=644 no_reads=0 ref_mismatch=0 other=0)