{
  "module": "analysis/18_full_reanalysis/metabolomics",
  "status": "PASS",
  "analysis_script_sha256": "c6aada1904ee08a857fd7bc5a37d5a40c2a0961258055a3b594f5f7ba49816e0",
  "started_at_utc": "2026-08-13T08:15:19.708826+00:00",
  "completed_at_utc": "2026-08-13T08:15:39.480137+00:00",
  "elapsed_seconds": 19.799371004104614,
  "command": "uv run --python 3.12 python analysis/18_full_reanalysis/metabolomics/run_metabolomics_full.py",
  "configuration": {
    "module": "18_full_reanalysis/metabolomics",
    "status": "fresh_full_reanalysis",
    "input_sample_info": "data/working/new_modalities_schema_20260806/零磁场节律/Metabolome_Sample_Info.xlsx",
    "input_intensity_matrix": "data/working/new_modalities_schema_20260806/零磁场节律-1/Metabolome_norm_intensity_featurespeaks.xlsx",
    "sampling_unit": "randomly collected faecal specimen row; animal and cage identity unavailable; independence cannot be verified",
    "canonical_recovery_mapping": {
      "R2week": "R+4",
      "R4week": "R+8"
    },
    "peak_unit": "one unique analytical signal per exact Type + MZ + RT group with identical intensity profile",
    "primary_qc_cv_percent": 30.0,
    "sensitivity_qc_cv_percent": 20.0,
    "QC20_sensitivity_method": "fixed 814-peak subset; exact reuse of feature-wise coefficients/raw p-values and BH recalculation within each declared QC20 family; community geometry fully refit",
    "QC20_sensitivity_scope": "primary 14-cell cosinor, seven stage field level/rhythm, four exposure DiD level/rhythm, two-week E8-anchored recovery P/S/Q/joint level/rhythm, direct R+8-vs-R+4 residual-gap level/rhythm, and seven-stage community PERMANOVA/PERMDISP; not stage-within-lineage, sex, endpoint/LOF tiers, or enrichment",
    "primary_transform": "log2 of supplied normalized positive intensity; no pseudocount and no CLR",
    "period_hours": 24.0,
    "primary_rhythm_model": "log2_intensity ~ sex + sin(2*pi*ZT/24) + cos(2*pi*ZT/24)",
    "covariance": "HC3 heteroskedasticity robust",
    "rhythm_test": "joint Wald test of sine/cosine terms (2 df)",
    "primary_bh_q": 0.05,
    "rhythm_fdr_family": "within each lineage-by-stage cell across all QC30 peaks",
    "zt24_sensitivity": "repeat every cell-level cosinor after excluding the separate ZT24 specimen rows",
    "zt0_sensitivity": "repeat every cell-level cosinor after excluding the separate ZT0 specimen rows",
    "categorical_ZT_lack_of_fit": {
      "model": "log2_intensity ~ sex + categorical means for ZT0/ZT6/ZT12/ZT18/ZT24",
      "boundary_test": "ZT24-ZT0, HC3 1 df",
      "single_harmonic_constraint": "mu0+mu12-mu6-mu18, HC3 1 df",
      "joint_test": "boundary plus single-harmonic constraint, HC3 2 df",
      "fdr_family": "within lineage-by-stage cell across all QC30 unique analytical peaks for each diagnostic"
    },
    "stage_references": {
      "exposure": "E0",
      "recovery": "E8"
    },
    "recovery_joint_test": "p_joint=max(p_P,p_S), BH across all peak-by-recovery-week rows",
    "recovery_directional_rule": "P*S<0 and abs(Q)<abs(P)",
    "recovery_rhythm_directional_rule": "dot(P,S)<0 and norm(Q)<norm(P)",
    "direct_recovery_progress_test": "(ZMF_R8-GMF_R8)-(ZMF_R4-GMF_R4), MESOR HC3 1df and sine/cosine HC3 2df with BH across QC-qualified unique peaks",
    "recovery_priority_log2_effect": 0.2630344058337938,
    "community_test": "Euclidean PERMANOVA-style pseudo-F on Pareto-scaled log2 peaks with field labels permuted within sex-by-ZT strata",
    "community_permutations": 9999,
    "community_fdr_family": "seven experimental stages",
    "permdisp": "sex-by-ZT-restricted RMS Euclidean distance-to-centroid test in the exact SVD sample space; BH across seven stages",
    "enrichment": {
      "annotation_levels": [
        "candidate_superclass",
        "candidate_class",
        "candidate_kegg_pathway"
      ],
      "background": "all QC30 unique analytical peaks",
      "test": "one-sided Fisher exact overrepresentation",
      "minimum_hit_peaks_per_term": 3,
      "fdr_family": "within each formal significant set by annotation level",
      "primary_q": 0.05,
      "candidate_rule": "a peak contributes at most once to a term even if multiple candidate annotations map to it"
    },
    "random_seed": 20260807
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  "inputs": {
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  "sampling_unit": "randomly collected faecal specimen row; animal and cage identity unavailable; independence cannot be verified",
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  "platform": "macOS-26.4.1-arm64-arm-64bit",
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}