{
  "status": "PASS",
  "module": "18_full_reanalysis_rna_context",
  "analysis_scope": "E8 secondary support only; no recovery inference; prior-publication overlap, not standalone story",
  "analysis_script_sha256": "2c30bf84d8970090f568022ea93d7d01f9ff7947b78c0a339a48664b9a83caea",
  "checks": [
    {
      "name": "allowed_input_count",
      "passed": true,
      "detail": "5 allowed workbooks"
    },
    {
      "name": "inputs_are_new_package_working_copies",
      "passed": true,
      "detail": "all five inputs reread from data/working/new_modalities_schema_20260806"
    },
    {
      "name": "forbidden_recover_inputs_absent",
      "passed": true,
      "detail": "Recover RNA workbooks not opened"
    },
    {
      "name": "main_metadata_samples",
      "passed": true,
      "detail": "n=684"
    },
    {
      "name": "main_rhythmic_static_partition",
      "passed": true,
      "detail": "rhythmic=600, static=84"
    },
    {
      "name": "scn_samples",
      "passed": true,
      "detail": "n=60"
    },
    {
      "name": "scn_famale_normalized",
      "passed": true,
      "detail": "source famale=30, canonical sex=['F', 'M']"
    },
    {
      "name": "main_design_cells_complete",
      "passed": true,
      "detail": "10 tissues x 2 fields x 2 sexes x 5 ZT x 3"
    },
    {
      "name": "static_design_cells_complete",
      "passed": true,
      "detail": "7 tissues x 2 fields x 2 sexes x 3"
    },
    {
      "name": "scn_design_cells_complete",
      "passed": true,
      "detail": "2 fields x 2 sexes x 5 ZT x 3"
    },
    {
      "name": "exact_tissue_and_model_partition",
      "passed": true,
      "detail": "tissues=18, rhythm cells=22, rhythmic field tissues=11, static=7"
    },
    {
      "name": "static_tissues_absent_from_rhythm_tables",
      "passed": true,
      "detail": "seven no-ZT tissues occur only in static field results"
    },
    {
      "name": "annotation_gene_counts",
      "passed": true,
      "detail": "main=52349, SCN=38882"
    },
    {
      "name": "raw_matrix_gene_counts",
      "passed": true,
      "detail": "main=57132, SCN=57132"
    },
    {
      "name": "raw_count_cells_complete_integer",
      "passed": true,
      "detail": "empty main=0, SCN=0; non-integer main=0, SCN=0"
    },
    {
      "name": "explicit_gene_id_join_complete",
      "passed": true,
      "detail": "every annotation gene_id found exactly once in raw counts; preallocated rows placed by key"
    },
    {
      "name": "raw_counts_nonnegative_int32",
      "passed": true,
      "detail": "max main=11655018, max SCN=1646032"
    },
    {
      "name": "full_raw_library_size_denominator",
      "passed": true,
      "detail": "CPM denominator sums all 57132 raw rows; annotated/full ratio main=0.999999984282-1.000000000000, SCN=0.999999981417-1.000000000000"
    },
    {
      "name": "primary_table_rows",
      "passed": true,
      "detail": "observed=358634, expected=358634"
    },
    {
      "name": "endpoint_and_lof_table_rows",
      "passed": true,
      "detail": "drop0=358634, drop24=358634, LOF=358634, tier=358634"
    },
    {
      "name": "field_table_rows",
      "passed": true,
      "detail": "rhythmic=179317/179317, static=115508/115508"
    },
    {
      "name": "core_table_unique_gene_keys",
      "passed": true,
      "detail": "gene_id unique within every tissue/field/test block"
    },
    {
      "name": "BH_recomputed_value_by_value",
      "passed": true,
      "detail": "245 within-family BH vectors recomputed exactly"
    },
    {
      "name": "conservative_tier_algebra",
      "passed": true,
      "detail": "primary & dropZT0 & dropZT24 q<0.05 and joint LOF q>=0.05"
    },
    {
      "name": "all_model_designs_full_rank",
      "passed": true,
      "detail": "every emitted HC3 block reports model_rank == n_parameters"
    },
    {
      "name": "q_values_in_range",
      "passed": true,
      "detail": "tracked 21 q columns"
    },
    {
      "name": "filter_QC_PCA_exact_rows",
      "passed": true,
      "detail": "filter=928815/928815, QC=744, PCA scores=744, loadings=180000/180000, explained=90"
    },
    {
      "name": "clock_set_enrichment_membership_exact_rows",
      "passed": true,
      "detail": "clock=464, sets=73, enrichment summary=219, all terms=1114709, membership=275047"
    },
    {
      "name": "rhythm_membership_carries_four_q_values",
      "passed": true,
      "detail": "columns=['primary_rhythm_q', 'dropZT0_rhythm_q', 'dropZT24_rhythm_q', 'joint_LOF_q'], rhythm membership rows=194411"
    },
    {
      "name": "all_gzip_streams_complete_and_deterministic",
      "passed": true,
      "detail": "gzip files=14, all read to EOF=True, all header mtime=0=True"
    },
    {
      "name": "fisher_odds_ratio_zero_over_zero_is_NA",
      "passed": true,
      "detail": "runtime assertion passed for 0 undefined 0/0 odds-ratio cells"
    },
    {
      "name": "no_forbidden_identity_columns",
      "passed": true,
      "detail": "metadata columns=['sample_id', 'source_sample_id', 'source_group', 'modality', 'tissue', 'field', 'sex', 'source_sex_label', 'ZT', 'replicate', 'design', 'stage', 'sampling_unit', 'analysis_scope']"
    },
    {
      "name": "no_A1_A12_samples",
      "passed": true,
      "detail": "no unmapped A1-A12 identifiers in canonical metadata"
    },
    {
      "name": "static_has_no_rhythm_labels",
      "passed": true,
      "detail": "all 7 static tissues restricted to sex-adjusted field model"
    },
    {
      "name": "core_clock_annotation_coverage",
      "passed": true,
      "detail": "covered=['Arntl', 'Clock', 'Cry1', 'Cry2', 'Dbp', 'Hlf', 'Npas2', 'Nr1d1', 'Nr1d2', 'Per1', 'Per2', 'Per3', 'Rora', 'Rorb', 'Rorc', 'Tef']"
    },
    {
      "name": "Arntl_Bmal1_alias_resolved",
      "passed": true,
      "detail": "requested Arntl mapped to supplied Bmal1 symbol at ENSMUSG00000055116"
    },
    {
      "name": "no_automatic_sample_deletion",
      "passed": true,
      "detail": "QC rows=744, automatic exclusions=0"
    },
    {
      "name": "npz_safe_string_dtypes",
      "passed": true,
      "detail": "18 matrices; strings load with allow_pickle=False"
    },
    {
      "name": "figure_triplicates",
      "passed": true,
      "detail": "9 files = 3 figures x PNG/SVG/PDF"
    },
    {
      "name": "figure_final_size_visual_QA",
      "passed": true,
      "detail": "3 figures at 183.0 mm and 600 dpi"
    },
    {
      "name": "scope_warning_exact",
      "passed": true,
      "detail": "E8 secondary support only; no recovery inference; prior-publication overlap, not standalone story; 744 sample columns explicitly not interpreted as 744 animals"
    }
  ],
  "q_ranges": {
    "primary:sex_q": {
      "n_total": 358634,
      "n_finite": 358633,
      "n_missing": 1,
      "min": 2.222035978047914e-43,
      "max": 0.9999885398831645,
      "valid_0_to_1": true
    },
    "primary:rhythm_q": {
      "n_total": 358634,
      "n_finite": 358633,
      "n_missing": 1,
      "min": 0.0,
      "max": 0.9999937143185146,
      "valid_0_to_1": true
    },
    "drop0:sex_q": {
      "n_total": 358634,
      "n_finite": 358631,
      "n_missing": 3,
      "min": 6.499862879600906e-37,
      "max": 0.999996313762795,
      "valid_0_to_1": true
    },
    "drop0:rhythm_q": {
      "n_total": 358634,
      "n_finite": 358631,
      "n_missing": 3,
      "min": 0.0,
      "max": 0.9999968022917111,
      "valid_0_to_1": true
    },
    "drop24:sex_q": {
      "n_total": 358634,
      "n_finite": 358633,
      "n_missing": 1,
      "min": 2.891890200635505e-32,
      "max": 0.9999946258498577,
      "valid_0_to_1": true
    },
    "drop24:rhythm_q": {
      "n_total": 358634,
      "n_finite": 358633,
      "n_missing": 1,
      "min": 0.0,
      "max": 0.9999995608612557,
      "valid_0_to_1": true
    },
    "lof:boundary_q": {
      "n_total": 358634,
      "n_finite": 358633,
      "n_missing": 1,
      "min": 1.1452634901846684e-20,
      "max": 1.0,
      "valid_0_to_1": true
    },
    "lof:harmonic_q": {
      "n_total": 358634,
      "n_finite": 358633,
      "n_missing": 1,
      "min": 1.1096649013104982e-12,
      "max": 0.9999999999999981,
      "valid_0_to_1": true
    },
    "lof:joint_LOF_q": {
      "n_total": 358634,
      "n_finite": 358633,
      "n_missing": 1,
      "min": 0.0,
      "max": 0.9999938846886108,
      "valid_0_to_1": true
    },
    "tier:rhythm_q": {
      "n_total": 358634,
      "n_finite": 358633,
      "n_missing": 1,
      "min": 0.0,
      "max": 0.9999937143185146,
      "valid_0_to_1": true
    },
    "tier:dropZT0_rhythm_q": {
      "n_total": 358634,
      "n_finite": 358631,
      "n_missing": 3,
      "min": 0.0,
      "max": 0.9999968022917111,
      "valid_0_to_1": true
    },
    "tier:dropZT24_rhythm_q": {
      "n_total": 358634,
      "n_finite": 358633,
      "n_missing": 1,
      "min": 0.0,
      "max": 0.9999995608612557,
      "valid_0_to_1": true
    },
    "tier:boundary_q": {
      "n_total": 358634,
      "n_finite": 358633,
      "n_missing": 1,
      "min": 1.1452634901846684e-20,
      "max": 1.0,
      "valid_0_to_1": true
    },
    "tier:harmonic_q": {
      "n_total": 358634,
      "n_finite": 358633,
      "n_missing": 1,
      "min": 1.1096649013104982e-12,
      "max": 0.9999999999999981,
      "valid_0_to_1": true
    },
    "tier:joint_LOF_q": {
      "n_total": 358634,
      "n_finite": 358633,
      "n_missing": 1,
      "min": 0.0,
      "max": 0.9999938846886108,
      "valid_0_to_1": true
    },
    "rhythmic_field:field_q": {
      "n_total": 179317,
      "n_finite": 179317,
      "n_missing": 0,
      "min": 2.2914710414113197e-19,
      "max": 0.9999971261669297,
      "valid_0_to_1": true
    },
    "rhythmic_field:field_x_rhythm_q": {
      "n_total": 179317,
      "n_finite": 179317,
      "n_missing": 0,
      "min": 2.099488025863666e-37,
      "max": 0.9999989877678537,
      "valid_0_to_1": true
    },
    "rhythmic_field:sex_q": {
      "n_total": 179317,
      "n_finite": 179317,
      "n_missing": 0,
      "min": 1.4744148254558866e-84,
      "max": 0.9999907526639646,
      "valid_0_to_1": true
    },
    "static_field:field_q": {
      "n_total": 115508,
      "n_finite": 115508,
      "n_missing": 0,
      "min": 3.866633576831061e-10,
      "max": 0.9999984881845744,
      "valid_0_to_1": true
    },
    "static_field:sex_q": {
      "n_total": 115508,
      "n_finite": 115508,
      "n_missing": 0,
      "min": 6.530298862126865e-16,
      "max": 0.9999875917759484,
      "valid_0_to_1": true
    },
    "annotation_enrichment:q_value": {
      "n_total": 1114709,
      "n_finite": 1114709,
      "n_missing": 0,
      "min": 2.913752942265993e-53,
      "max": 1.0,
      "valid_0_to_1": true
    }
  },
  "self_audit": {
    "bh_exact": true,
    "bh_checks": 245,
    "unique_gene_keys": true,
    "tier_algebra": true,
    "design_full_rank": true
  },
  "figure_visual_qa": {
    "status": "PASS",
    "scope": "three active E8 RNA figures; final-size clipping and same-axes text audit",
    "figure_width_mm": 183.0,
    "png_dpi": 600,
    "figures": {
      "figure_week8_rna_qc": {
        "visible_text_items": 48,
        "outside_canvas": [],
        "same_axes_text_overlaps": [],
        "status": "PASS",
        "physical_width_mm": 183.0,
        "dpi": 600,
        "png_pixels": [
          4322,
          2748
        ],
        "triplet_nonempty": true
      },
      "figure_week8_rna_inference_landscape": {
        "visible_text_items": 29,
        "outside_canvas": [],
        "same_axes_text_overlaps": [],
        "status": "PASS",
        "physical_width_mm": 183.0,
        "dpi": 600,
        "png_pixels": [
          4322,
          2892
        ],
        "triplet_nonempty": true
      },
      "figure_week8_rna_core_clock_audit": {
        "visible_text_items": 53,
        "outside_canvas": [],
        "same_axes_text_overlaps": [],
        "status": "PASS",
        "physical_width_mm": 183.0,
        "dpi": 600,
        "png_pixels": [
          4322,
          2688
        ],
        "triplet_nonempty": true
      }
    },
    "generated_at_utc": "2026-08-13T18:37:28.680112+00:00"
  },
  "gzip_uncompressed_bytes": {
    "formal_significant_set_membership.csv.gz": 52369874,
    "gene_annotation_main.csv.gz": 33490776,
    "gene_annotation_scn.csv.gz": 29666930,
    "gene_set_enrichment_all_terms.csv.gz": 248986629,
    "pca_loadings.csv.gz": 10338178,
    "pca_scores.csv.gz": 95408,
    "rhythm_categorical_ZT_LOF.csv.gz": 70439694,
    "rhythm_conservative_tier.csv.gz": 80592763,
    "rhythm_cosinor_dropZT0.csv.gz": 78931439,
    "rhythm_cosinor_dropZT24.csv.gz": 79560237,
    "rhythm_cosinor_primary.csv.gz": 78622641,
    "rhythmic_field_mesor_interaction.csv.gz": 41688632,
    "static_tissue_field_effect.csv.gz": 16147062,
    "tissue_gene_expression_filter.csv.gz": 66582957
  },
  "table_rows": {
    "filter": 928815,
    "pca_scores": 744,
    "pca_loadings": 180000,
    "primary": 358634,
    "drop0": 358634,
    "drop24": 358634,
    "lof": 358634,
    "tier": 358634,
    "field": 179317,
    "static": 115508,
    "membership": 275047
  },
  "raw_count_cell_audit": {
    "main_empty_cells": 0,
    "main_non_integer_cells": 0,
    "scn_empty_cells": 0,
    "scn_non_integer_cells": 0
  },
  "input_shapes": {
    "main_metadata_samples": 684,
    "scn_samples": 60,
    "main_raw_genes": 57132,
    "main_raw_samples": 684,
    "main_annotation_genes": 52349,
    "scn_raw_genes": 57132,
    "scn_raw_samples": 60,
    "scn_annotation_genes": 38882
  },
  "library_size_audit": {
    "denominator": "per-sample sum over all 57,132 raw gene rows before restriction to the annotation gene set",
    "main_annotation_included_to_full_ratio_min": 0.9999999842823609,
    "main_annotation_included_to_full_ratio_max": 1.0,
    "scn_annotation_included_to_full_ratio_min": 0.9999999814165761,
    "scn_annotation_included_to_full_ratio_max": 1.0
  },
  "generated_at_utc": "2026-08-13T18:37:29.589107+00:00",
  "run_manifest_sha256": "09a8cc8466663fdc07ee805a92e72dd3edbfcb562dd2f720922ebe0e5f0a06e0",
  "manifest_written_before_final_validation": true,
  "figure_only_redraw_at_utc": "2026-08-15T08:19:29.822771+00:00"
}