.command.log - Workdir - SOMATIC_CNV_REF_BUILDER:SOMA_CNV_BUILD_REFERENCE (build_reference)

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Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/f2f03a1d68f5f8721158aa811601c9/.command.log
Size: 8.3 KB
Task: SOMATIC_CNV_REF_BUILDER:SOMA_CNV_BUILD_REFERENCE (build_reference)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/451b13a415051f2608900280e3a2ef/869_XA6-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/27d85382aac6b599551fdf6efcb70a/869_NNC-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/258ef2bdaa08997b0f9f447ca761d3/869_HUS-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/7fcbcad42cc5136adf5b5e8f02a2ce/659_btT-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/03b7537fde43f16d00b6c68d10b9cd/659_esc-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/60/9c482a92ebe6f6f913cb942dcd0228/manifest.tsv
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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/46f3dec819e9d5e73fe83e9b53cca5/869_OC5-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/f2f03a1d68f5f8721158aa811601c9/.command.run
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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/cdbe1c74b37045d732655932495918/869_MMQ-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/f2f03a1d68f5f8721158aa811601c9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/96826b69e6afd41502db9c38fec79f/659_c6S-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/f4374b0029be97b5103588615b6d58/869_EH0-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/2df676a6c7e2d1076dfa6afc1f9f7e/869_SL4-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
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==> STAGING COMPLETE (49 inputs)

Blood manifest: 46 samples
Loaded 21,729,756 rows from 46 blood samples in 25.6s
GC reference: 472,386 probes
  Sex chrom homology mask: 1494 probes
  Pass 1: 4-feat blood GAM (16 workers)...
    20/46 blood samples, 25s, R²=0.4368
    40/46 blood samples, 38s, R²=0.4342
    46/46 blood samples, 40s, R²=0.4312
    Sex: 28 female, 18 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: 471,485/472,386 valid probes
  Preliminary 5-feat GAM on blood (16 workers)...
    20/46 blood prelim 5-feat, 37s, R²=0.9379
    40/46 blood prelim 5-feat, 57s, R²=0.9342
    46/46 blood prelim 5-feat, 57s, R²=0.9346
/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: 16,591 masked (3.5%) — 10,786 low cov, 7,840 high var, 3,994 extreme
Wrote batch_reference.parquet (472,386 probes) to ./batch_reference.parquet
Wrote sex_calls.csv (46 samples) to ./sex_calls.csv
Wrote feature_stats.csv (46 samples) to ./feature_stats.csv
Build reference complete in 243.6s total