Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/d4aea4b49bd13578f630ddb1a86e59/HCC1395_BL_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/02b8530b26a3f500f7d88924dad3a1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/34f88a089fc913355767c9231b057c/Sig_18_Blood_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/02b8530b26a3f500f7d88924dad3a1/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/a0/43ad5813c8e230f82e5341826283ea/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