{ "status": "PASS", "module": "analysis/18_full_reanalysis/metabolomics", "analysis_script_sha256": "c6aada1904ee08a857fd7bc5a37d5a40c2a0961258055a3b594f5f7ba49816e0", "started_at_utc": "2026-08-13T08:15:19.708826+00:00", "input_files": { "data/working/new_modalities_schema_20260806/零磁场节律/Metabolome_Sample_Info.xlsx": { "bytes": 33315, "sha256": "97e0ffa82f34889a771af5c9dc96104cfa5be35b5fad8fb610eb150679530f52" }, "data/working/new_modalities_schema_20260806/零磁场节律-1/Metabolome_norm_intensity_featurespeaks.xlsx": { "bytes": 29787254, "sha256": "2c837496e61d52084b162295c3e2e24e7a5d22da22cdf223cd298edc2ef40829" } }, "upstream_statistical_outputs_used": [], "upstream_output_policy": "analysis/12-17 outputs were not read; comparisons, if any, occur only after this run", "sample_design": { "biological_samples": 840, "qc_samples": 93, "matrix_biological_ids_exactly_match_metadata": true, "canonical_recovery_mapping": { "R2week": "R+4", "R4week": "R+8" }, "R_plus_4_samples": 120, "R_plus_8_samples": 120, "all_lineage_stage_ZT_sex_cells_n6": true, "scheduled_ZT_labels": [ 0, 6, 12, 18, 24 ], "unique_24h_phase_coordinates": [ 0, 6, 12, 18 ], "QC_numeric_range": [ 1, 97 ], "missing_QC_numbers_in_range": [ 86, 87, 88, 89 ], "sampling_unit": "randomly collected faecal specimen row; animal and cage identity unavailable; independence cannot be verified", "independence_verifiable": false, "paired_or_random_animal_model": false }, "peak_collapse": { "candidate_annotation_rows": 2232, "independent_peaks": 1171, "ambiguous_peaks": 495, "rows_in_ambiguous_groups": 1556, "maximum_candidates_per_peak": 5, "all_group_profiles_exactly_equal_across_933_samples": true }, "intensity": { "raw_normalized_intensity_range": [ 58400.8730886534, 164231064156.137 ], "all_values_finite_and_positive": true, "transform": "log2 without pseudocount; no CLR", "primary_QC_CV_percent": 30.0, "QC20_sensitivity_QC_CV_percent": 20.0, "independent_peaks_pass_QC30": 1171, "independent_peaks_pass_QC20": 814, "QC30_peaks_filtered_from_QC20_subuniverse": 357, "QC_CV_median_percent": 14.946279837488824, "QC_CV_max_percent": 29.98501029177409 }, "models": { "all_design_matrices_full_rank": true, "design_rank_checks": [ { "model": "cosinor_GMF_E0_primary_all_specimen_rows", "n_samples": 60, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_GMF_E2_primary_all_specimen_rows", "n_samples": 60, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_GMF_E4_primary_all_specimen_rows", "n_samples": 60, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_GMF_E6_primary_all_specimen_rows", "n_samples": 60, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_GMF_E8_primary_all_specimen_rows", "n_samples": 60, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_GMF_R+4_primary_all_specimen_rows", "n_samples": 60, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_GMF_R+8_primary_all_specimen_rows", "n_samples": 60, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_ZMF_E0_primary_all_specimen_rows", "n_samples": 60, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_ZMF_E2_primary_all_specimen_rows", "n_samples": 60, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_ZMF_E4_primary_all_specimen_rows", "n_samples": 60, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_ZMF_E6_primary_all_specimen_rows", "n_samples": 60, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_ZMF_E8_primary_all_specimen_rows", "n_samples": 60, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_ZMF_R+4_primary_all_specimen_rows", "n_samples": 60, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_ZMF_R+8_primary_all_specimen_rows", "n_samples": 60, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_GMF_E0_exclude_ZT24", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_GMF_E2_exclude_ZT24", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_GMF_E4_exclude_ZT24", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_GMF_E6_exclude_ZT24", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_GMF_E8_exclude_ZT24", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_GMF_R+4_exclude_ZT24", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_GMF_R+8_exclude_ZT24", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_ZMF_E0_exclude_ZT24", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_ZMF_E2_exclude_ZT24", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_ZMF_E4_exclude_ZT24", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_ZMF_E6_exclude_ZT24", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_ZMF_E8_exclude_ZT24", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_ZMF_R+4_exclude_ZT24", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_ZMF_R+8_exclude_ZT24", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_GMF_E0_exclude_ZT0", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_GMF_E2_exclude_ZT0", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_GMF_E4_exclude_ZT0", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_GMF_E6_exclude_ZT0", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_GMF_E8_exclude_ZT0", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_GMF_R+4_exclude_ZT0", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_GMF_R+8_exclude_ZT0", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_ZMF_E0_exclude_ZT0", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_ZMF_E2_exclude_ZT0", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_ZMF_E4_exclude_ZT0", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_ZMF_E6_exclude_ZT0", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_ZMF_E8_exclude_ZT0", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_ZMF_R+4_exclude_ZT0", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "cosinor_ZMF_R+8_exclude_ZT0", "n_samples": 48, "n_parameters": 4, "rank": 4, "full_rank": true }, { "model": "categorical_ZT_LOF_GMF_E0", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "categorical_ZT_LOF_GMF_E2", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "categorical_ZT_LOF_GMF_E4", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "categorical_ZT_LOF_GMF_E6", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "categorical_ZT_LOF_GMF_E8", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "categorical_ZT_LOF_GMF_R+4", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "categorical_ZT_LOF_GMF_R+8", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "categorical_ZT_LOF_ZMF_E0", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "categorical_ZT_LOF_ZMF_E2", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "categorical_ZT_LOF_ZMF_E4", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "categorical_ZT_LOF_ZMF_E6", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "categorical_ZT_LOF_ZMF_E8", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "categorical_ZT_LOF_ZMF_R+4", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "categorical_ZT_LOF_ZMF_R+8", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "field_E0", "n_samples": 120, "n_parameters": 7, "rank": 7, "full_rank": true }, { "model": "field_E2", "n_samples": 120, "n_parameters": 7, "rank": 7, "full_rank": true }, { "model": "field_E4", "n_samples": 120, "n_parameters": 7, "rank": 7, "full_rank": true }, { "model": "field_E6", "n_samples": 120, "n_parameters": 7, "rank": 7, "full_rank": true }, { "model": "field_E8", "n_samples": 120, "n_parameters": 7, "rank": 7, "full_rank": true }, { "model": "field_R+4", "n_samples": 120, "n_parameters": 7, "rank": 7, "full_rank": true }, { "model": "field_R+8", "n_samples": 120, "n_parameters": 7, "rank": 7, "full_rank": true }, { "model": "stage_GMF_E2_vs_E0", "n_samples": 120, "n_parameters": 7, "rank": 7, "full_rank": true }, { "model": "stage_GMF_E4_vs_E0", "n_samples": 120, "n_parameters": 7, "rank": 7, "full_rank": true }, { "model": "stage_GMF_E6_vs_E0", "n_samples": 120, "n_parameters": 7, "rank": 7, "full_rank": true }, { "model": "stage_GMF_E8_vs_E0", "n_samples": 120, "n_parameters": 7, "rank": 7, "full_rank": true }, { "model": "stage_GMF_R+4_vs_E8", "n_samples": 120, "n_parameters": 7, "rank": 7, "full_rank": true }, { "model": "stage_GMF_R+8_vs_E8", "n_samples": 120, "n_parameters": 7, "rank": 7, "full_rank": true }, { "model": "stage_GMF_R+8_vs_R+4", "n_samples": 120, "n_parameters": 7, "rank": 7, "full_rank": true }, { "model": "stage_ZMF_E2_vs_E0", "n_samples": 120, "n_parameters": 7, "rank": 7, "full_rank": true }, { "model": "stage_ZMF_E4_vs_E0", "n_samples": 120, "n_parameters": 7, "rank": 7, "full_rank": true }, { "model": "stage_ZMF_E6_vs_E0", "n_samples": 120, "n_parameters": 7, "rank": 7, "full_rank": true }, { "model": "stage_ZMF_E8_vs_E0", "n_samples": 120, "n_parameters": 7, "rank": 7, "full_rank": true }, { "model": "stage_ZMF_R+4_vs_E8", "n_samples": 120, "n_parameters": 7, "rank": 7, "full_rank": true }, { "model": "stage_ZMF_R+8_vs_E8", "n_samples": 120, "n_parameters": 7, "rank": 7, "full_rank": true }, { "model": "stage_ZMF_R+8_vs_R+4", "n_samples": 120, "n_parameters": 7, "rank": 7, "full_rank": true }, { "model": "exposure_field_gap_DiD_E2_vs_E0", "n_samples": 240, "n_parameters": 13, "rank": 13, "full_rank": true }, { "model": "exposure_field_gap_DiD_E4_vs_E0", "n_samples": 240, "n_parameters": 13, "rank": 13, "full_rank": true }, { "model": "exposure_field_gap_DiD_E6_vs_E0", "n_samples": 240, "n_parameters": 13, "rank": 13, "full_rank": true }, { "model": "exposure_field_gap_DiD_E8_vs_E0", "n_samples": 240, "n_parameters": 13, "rank": 13, "full_rank": true }, { "model": "recovery_R4", "n_samples": 240, "n_parameters": 13, "rank": 13, "full_rank": true }, { "model": "recovery_R8", "n_samples": 240, "n_parameters": 13, "rank": 13, "full_rank": true }, { "model": "direct_recovery_progress_R8_minus_R4", "n_samples": 240, "n_parameters": 13, "rank": 13, "full_rank": true }, { "model": "sex_GMF_E0", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "sex_GMF_E2", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "sex_GMF_E4", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "sex_GMF_E6", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "sex_GMF_E8", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "sex_GMF_R+4", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "sex_GMF_R+8", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "sex_ZMF_E0", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "sex_ZMF_E2", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "sex_ZMF_E4", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "sex_ZMF_E6", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "sex_ZMF_E8", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "sex_ZMF_R+4", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true }, { "model": "sex_ZMF_R+8", "n_samples": 60, "n_parameters": 6, "rank": 6, "full_rank": true } ], "primary_cosinor_rows": 16394, "ZT24_sensitivity_rows": 16394, "ZT0_sensitivity_rows": 16394, "primary_cosinor_cells": 14, "primary_cosinor_BH_q005_only": true, "categorical_ZT_LOF_rows": 16394, "categorical_ZT_LOF_cells": 14, "conservative_tier_rows": 16394, "field_rows": 8197, "stage_contrast_rows": 16394, "exposure_field_gap_DiD_rows": 4684, "recovery_level_rows": 2342, "recovery_rhythm_rows": 2342, "recovery_progress_rows": 1171, "sex_rows": 16394, "recovery_Q_equals_P_plus_S_max_abs_error": 3.552713678800501e-15, "recovery_rhythm_vector_Q_equals_P_plus_S_max_abs_error": 4.440892098500626e-16, "field_interpretation_by_stage": { "E0": "baseline allocation/group gap", "E2": "stage-matched current-field contrast", "E4": "stage-matched current-field contrast", "E6": "stage-matched current-field contrast", "E8": "stage-matched current-field contrast", "R+4": "origin-lineage residual contrast; both branches in GMF", "R+8": "origin-lineage residual contrast; both branches in GMF" }, "primary_exact_BH_checks": { "cosinor": true, "field_mesor": true, "field_rhythm": true, "DiD_mesor": true, "DiD_rhythm": true, "recovery_level_joint": true, "recovery_rhythm_joint": true, "recovery_progress_mesor": true, "recovery_progress_rhythm": true, "community_PERMANOVA": true, "community_PERMDISP": true }, "all_q_values_in_0_1": true }, "QC20_sensitivity": { "method": "exact reuse of the same feature-wise HC3 coefficients/raw p-values followed by BH recalculation in the fixed 814-peak family; community geometry fully refit", "QC20_peak_count": 814, "QC30_only_peaks_filtered": 357, "peak_sets_exactly_match_catalog_QC20": true, "row_and_unique_key_checks": { "cosinor_14_cells_x_814": true, "field_7_stages_x_814": true, "DiD_4_targets_x_814": true, "recovery_level_2_weeks_x_814": true, "recovery_rhythm_2_weeks_x_814": true, "recovery_progress_1_contrast_x_814": true }, "exact_BH_recalculation_checks": { "cosinor": true, "field_mesor": true, "field_rhythm": true, "DiD_mesor": true, "DiD_rhythm": true, "recovery_progress_mesor": true, "recovery_progress_rhythm": true, "recovery_level_P": true, "recovery_level_S": true, "recovery_level_Q": true, "recovery_level_joint": true, "recovery_rhythm_P": true, "recovery_rhythm_S": true, "recovery_rhythm_Q": true, "recovery_rhythm_joint": true }, "feature_raw_p_and_effect_exact_reuse_checks": { "cosinor_raw_p_and_effects": true, "field_raw_p_and_effects": true, "DiD_raw_p_and_effects": true, "recovery_level_raw_p_and_effects": true, "recovery_rhythm_raw_p_and_effects": true, "recovery_progress_raw_p_and_effects": true }, "community_refit_checks": { "PERMANOVA_seven_stages_9999_permutations_BH": true, "PERMDISP_seven_stages_9999_permutations_BH": true }, "summary_rows": 56, "expected_summary_rows": 56, "feature_effect_values_exactly_reused": true, "community_refit_in_QC20_peak_space": true, "all_q_values_in_0_1": true }, "community": { "method": "field labels permuted within sex-by-exact-ZT strata", "permutations_per_stage": 9999, "stages": 7, "BH_across_seven_stages": true, "permdisp_implemented": true, "permdisp_variant": "restricted RMS Euclidean distance-to-centroid test in exact SVD sample space", "QC20_peak_space_refit": true, "primary_exact_BH_checks": { "community_PERMANOVA": true, "community_PERMDISP": true }, "warning": "centroid and dispersion tests remain exploratory specimen-row evidence; animal/cage identity and independence are unverifiable" }, "candidate_annotation_enrichment": { "background_independent_peaks": 1171, "peak_term_rows": 3359, "formal_significant_sets": 48, "formal_significant_membership_rows": 20747, "enrichment_rows": 7296, "summary_rows": 144, "test": "one-sided Fisher exact; BH within significant set by annotation level", "minimum_hit_peaks_for_call": 3, "unit": "unique Type/MZ/RT analytical peak; duplicate candidate names never counted twice within a term", "warning": "candidate annotations only; ConfidenceScore definition and structural identification level unavailable", "all_enrichment_q_values_finite_0_1": true }, "outputs": { "npz_orientation": "sample_by_peak", "canonical_metadata": "outputs/canonical_sample_metadata.csv", "log2_matrix": "outputs/log2_intensity_qc30.npz", "peak_catalog": "outputs/peak_catalog.csv.gz", "figures": [ "figures/figure_metabolomics_qc_pca.png", "figures/figure_metabolomics_qc_pca.svg", "figures/figure_metabolomics_qc_pca.pdf", "figures/figure_metabolomics_population_inference.png", "figures/figure_metabolomics_population_inference.svg", "figures/figure_metabolomics_population_inference.pdf", "figures/figure_metabolomics_recovery_progress.png", "figures/figure_metabolomics_recovery_progress.svg", "figures/figure_metabolomics_recovery_progress.pdf" ], "results_summary": "RESULTS_SUMMARY.md", "QC20_sensitivity_summary": "outputs/qc20_sensitivity_summary.csv", "all_gzip_streams_read_to_EOF": true, "gzip_uncompressed_bytes": { "candidate_annotation_enrichment_all_terms.csv.gz": 2629395, "candidate_peak_annotation_terms.csv.gz": 658325, "cosinor_24h_exclude_ZT0_sensitivity.csv.gz": 8260474, "cosinor_24h_exclude_ZT24_sensitivity.csv.gz": 8278154, "cosinor_24h_primary.csv.gz": 8491395, "cosinor_ZT24_sensitivity_comparison.csv.gz": 3562904, "cosinor_categorical_ZT_lack_of_fit.csv.gz": 11836137, "cosinor_conservative_tiers.csv.gz": 6347750, "exposure_field_gap_DiD.csv.gz": 2526216, "field_mesor_and_rhythm_contrasts.csv.gz": 3809816, "formal_significant_set_membership.csv.gz": 1955402, "lineage_stage_contrasts.csv.gz": 6279902, "pca_loadings.csv.gz": 524955, "pca_scores.csv.gz": 661697, "peak_catalog.csv.gz": 455469, "qc20_sensitivity_cosinor.csv.gz": 6263628, "qc20_sensitivity_exposure_DiD.csv.gz": 1940264, "qc20_sensitivity_field.csv.gz": 2970707, "qc20_sensitivity_recovery_level.csv.gz": 951079, "qc20_sensitivity_recovery_progress.csv.gz": 549570, "qc20_sensitivity_recovery_rhythm.csv.gz": 1081700, "recovery_P_S_Q_mesor_contrasts.csv.gz": 1089122, "recovery_P_S_Q_rhythm_contrasts.csv.gz": 1290571, "recovery_R8_vs_R4_direct_contrasts.csv.gz": 723814, "sex_mesor_and_rhythm_interactions.csv.gz": 8218330 } }, "environment": { "python": "3.12.12", "numpy": "2.0.2", "pandas": "2.3.3", "scipy": "1.13.1", "scikit_learn": "1.6.1", "openpyxl": "3.1.5", "matplotlib": "3.9.4" }, "completed_at_utc": "2026-08-13T08:15:39.480137+00:00", "elapsed_seconds": 19.817006826400757, "run_manifest_sha256": "467e9a998edb428d804d62e9009b1999085712b6aa9924267518d9ba224e9936", "manifest_written_before_final_validation": true, "figure_only_redraw_at_utc": "2026-08-13T18:29:39.400605+00:00" }