{
  "date": "2026-10-02",
  "version": "3.5.2",
  "dataset": "bundled three-sample CAMI reviewer inputs",
  "output_directory": "/data/users/ryan/MetaPathways_AppNote/mp352-conda-reviewer/output-taxonomy",
  "workflow_tasks": 51,
  "all_tasks_successful": true,
  "sqlite_integrity": "ok",
  "foreign_key_violations": 0,
  "report_schema": 3,
  "pathway_tools_executed": false,
  "samples": [
    {
      "sample": "Gastrointestinal_5",
      "assembly_contigs": 3,
      "read_pairs": 2326,
      "CDS": 140,
      "abundance_rows": 155,
      "genome_bins": 3,
      "reference_hit_taxonomy_rows": 311,
      "primary_rows_with_hit_taxonomy": 68,
      "orf_tpm_sum": 1000000.0000000001,
      "contig_tpm_sum": 1000000.0399999999,
      "unannotated_placeholders_are_only_RNA": true,
      "feature_counts": {
        "CDS": 140,
        "tRNA": 12,
        "rRNA": 3
      }
    },
    {
      "sample": "Skin_28",
      "assembly_contigs": 3,
      "read_pairs": 3000,
      "CDS": 117,
      "abundance_rows": 121,
      "genome_bins": 3,
      "reference_hit_taxonomy_rows": 221,
      "primary_rows_with_hit_taxonomy": 63,
      "orf_tpm_sum": 1000000.0000000006,
      "contig_tpm_sum": 1000000.06,
      "unannotated_placeholders_are_only_RNA": true,
      "feature_counts": {
        "CDS": 117,
        "tRNA": 4
      }
    },
    {
      "sample": "Urogenital_22",
      "assembly_contigs": 3,
      "read_pairs": 3000,
      "CDS": 136,
      "abundance_rows": 145,
      "genome_bins": 3,
      "reference_hit_taxonomy_rows": 244,
      "primary_rows_with_hit_taxonomy": 68,
      "orf_tpm_sum": 999999.9999999998,
      "contig_tpm_sum": 999999.93,
      "unannotated_placeholders_are_only_RNA": true,
      "feature_counts": {
        "CDS": 136,
        "tRNA": 6,
        "rRNA": 3
      }
    }
  ],
  "checks_passed": [
    "paired FASTQ identifiers and sequence/quality lengths",
    "all CDS represented in primary annotations",
    "every source abundance value matches the wide explorer",
    "no unavailable ORF coverage converted to zero",
    "functional taxonomy joined by sample/ORF/database/target",
    "primary taxonomy agrees with selected reference hit",
    "all primary annotation placeholders explained by RNA features",
    "three contigs assigned to three genome bins per sample",
    "TPM sums approximately one million separately for ORF and contig features",
    "51 Nextflow trace rows completed with exit zero"
  ],
  "expected_messages": [
    "Two Skin_28 BLAST empty-query warnings: no rRNA queries in this subset",
    "28 RNA features have abundance but no primary protein annotation",
    "PGDBs unavailable because --skip_ptools was used",
    "HTTP 404s from report browsing, not workflow failures"
  ],
  "report_notes_after_cleanup": 0,
  "report_cleanup": "Removed generic abundance notices and excluded explicitly identified tRNA/rRNA features from missing protein annotation warnings; all 430 abundance rows retained."
}