Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/30e1885381d933dc0b5e87c82cdd54/HCC1395_BL_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/5f65c3c45ace56ba7383f307d11ac9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/5a6da3bef30d8d51507d42e4a3af35/Sig_18_Blood_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/5f65c3c45ace56ba7383f307d11ac9/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/70/c52b87e498b9d146d6a5757dc881cf/manifest.tsv
==> STAGING COMPLETE (5 inputs)

Blood manifest: 2 samples
Loaded 9,638 rows from 2 blood samples in 0.0s
GC reference: 4,819 probes
  Pass 1: 4-feat blood GAM (16 workers)...
    2/2 blood samples, 0s, R²=0.5551
    Excluded 2 samples with chrX < 0.1 (data quality)
    Probe coverage: 4,819/4,819 valid probes
  Preliminary 5-feat GAM on blood (16 workers)...
    2/2 blood prelim 5-feat, 0s, R²=0.9568
    Probe mask: 187 masked (3.9%) — 66 low cov, 139 high var, 25 extreme
Wrote batch_reference.parquet (4,819 probes) to ./batch_reference.parquet
Wrote sex_calls.csv (2 samples) to ./sex_calls.csv
Wrote feature_stats.csv (2 samples) to ./feature_stats.csv
Build reference complete in 1.1s total