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==> STAGING COMPLETE (91 inputs)
Blood manifest: 88 samples
Loaded 41,569,968 rows from 88 blood samples in 50.2s
GC reference: 472,386 probes
Sex chrom homology mask: 1494 probes
Pass 1: 4-feat blood GAM (16 workers)...
20/88 blood samples, 25s, R²=0.4293
40/88 blood samples, 38s, R²=0.4231
60/88 blood samples, 52s, R²=0.4083
80/88 blood samples, 65s, R²=0.4827
88/88 blood samples, 71s, R²=0.4224
Sex: 49 female, 39 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: 471,842/472,386 valid probes
Preliminary 5-feat GAM on blood (16 workers)...
20/88 blood prelim 5-feat, 35s, R²=0.9241
40/88 blood prelim 5-feat, 53s, R²=0.9246
60/88 blood prelim 5-feat, 71s, R²=0.9254
80/88 blood prelim 5-feat, 91s, R²=0.9211
88/88 blood prelim 5-feat, 101s, R²=0.9092
/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: 17,944 masked (3.8%) — 10,666 low cov, 10,739 high var, 4,821 extreme
Wrote batch_reference.parquet (472,386 probes) to ./batch_reference.parquet
Wrote sex_calls.csv (88 samples) to ./sex_calls.csv
Wrote feature_stats.csv (88 samples) to ./feature_stats.csv
Build reference complete in 473.8s total