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==> STAGING COMPLETE (73 inputs)

Blood manifest: 70 samples
Loaded 33,067,020 rows from 70 blood samples in 39.8s
GC reference: 472,386 probes
  Sex chrom homology mask: 1494 probes
  Pass 1: 4-feat blood GAM (16 workers)...
    20/70 blood samples, 28s, R²=0.5188
    40/70 blood samples, 45s, R²=0.5438
    60/70 blood samples, 59s, R²=0.5247
    70/70 blood samples, 63s, R²=0.5221
    Sex: 45 female, 25 male, 0 unknown
/usr/local/bin/build_norm_reference.py:247: RuntimeWarning: All-NaN slice encountered
  probe_coverage_median = np.nanmedian(blood_matrix, axis=1)
/usr/local/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1593: RuntimeWarning: All-NaN slice encountered
  return fnb._ureduce(a,
    Probe coverage: 471,826/472,386 valid probes
  Preliminary 5-feat GAM on blood (16 workers)...
    20/70 blood prelim 5-feat, 38s, R²=0.9534
    40/70 blood prelim 5-feat, 56s, R²=0.9477
    60/70 blood prelim 5-feat, 76s, R²=0.9515
    70/70 blood prelim 5-feat, 87s, R²=0.9433
/usr/local/bin/build_norm_reference.py:335: RuntimeWarning: All-NaN slice encountered
  prelim_median = np.nanmedian(prelim_matrix, axis=1)
/usr/local/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1593: RuntimeWarning: All-NaN slice encountered
  return fnb._ureduce(a,
    Probe mask: 8,536 masked (1.8%) — 4,107 low cov, 4,985 high var, 1,882 extreme
Wrote batch_reference.parquet (472,386 probes) to ./batch_reference.parquet
Wrote sex_calls.csv (70 samples) to ./sex_calls.csv
Wrote feature_stats.csv (70 samples) to ./feature_stats.csv
Build reference complete in 380.6s total