Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/43fcf3c754ea8170f4aec27b54bce8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/249a25a25cef4e7191b8fe603f4e81/Sig_18_Blood_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/43fcf3c754ea8170f4aec27b54bce8/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/3a/331626282aee32bc0def7735858475/manifest.tsv
==> STAGING COMPLETE (4 inputs)

Blood manifest: 1 samples
Loaded 472,386 rows from 1 blood samples in 0.4s
GC reference: 472,386 probes
  Sex chrom homology mask: 1494 probes
  Pass 1: 4-feat blood GAM (16 workers)...
    1/1 blood samples, 1s, R²=nan
    Excluded 1 samples with chrX < 0.1 (data quality)
/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: 0/472,386 valid probes
  Preliminary 5-feat GAM on blood (16 workers)...
    1/1 blood prelim 5-feat, 0s, R²=nan
/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: 0 masked (0.0%) — 0 low cov, 0 high var, 0 extreme
Wrote batch_reference.parquet (472,386 probes) to ./batch_reference.parquet
Wrote sex_calls.csv (1 samples) to ./sex_calls.csv
Wrote feature_stats.csv (1 samples) to ./feature_stats.csv
Build reference complete in 12.2s total