Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/d93a355abbc6960314dc5727469b93/1029_16G-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/e12f0e0aeec92dadcc9d34dbd61a5d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/5eb719b94ddc6b60cdb714a722c37a/1029_11H-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/3b484dc7af178463529431786a3cb8/1029_01S-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/a7/bc6401416532059f6f3dcac24db094/manifest.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/e12f0e0aeec92dadcc9d34dbd61a5d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/9334e3406d502b65c51c54b75ed68d/1029_0W2-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/f380130d4b4f847a289135386b37e8/1029_0I-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz
==> STAGING COMPLETE (8 inputs)

Blood manifest: 5 samples
Loaded 2,361,930 rows from 5 blood samples in 3.0s
GC reference: 472,386 probes
  Sex chrom homology mask: 1494 probes
  Pass 1: 4-feat blood GAM (16 workers)...
    5/5 blood samples, 15s, R²=0.4881
    Sex: 1 female, 4 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: 471,724/472,386 valid probes
  Preliminary 5-feat GAM on blood (16 workers)...