Output Files

All outputs are written into your sample directory under output_fdb/ and/or output_gen/, depending on which analysis modes were enabled.

Directory Structure

my_directory/
├── ko_taxonomy_abundance.csv
├── noquote_ko.txt
├── foodb_foods_dataframe.csv
├── kegg_organisms_dataframe.csv
├── run_info.txt                         # pipeline metadata for this run
├── output_fdb/                          # FooDB-based analysis outputs
│   ├── food_meta.csv
│   ├── food_compound_report.html
│   ├── microbe_compound_report.html     # only if --include-orgs and --n-weights
│   ├── AMON_output/
│   │   ├── AMON_log.txt
│   │   ├── gene_set_1_enrichment.tsv
│   │   ├── kegg_mapper.tsv
│   │   ├── origin_table.tsv
│   │   ├── enrichment_heatmap.png
│   │   ├── co_dict.json
│   │   ├── ko_dict.json
│   │   └── rn_dict.json
│   └── graph/
│       ├── M_nodes_df.csv
│       ├── M_edges_df.csv
│       ├── M_AbundanceDistribution.png
│       ├── M_FoodFrequencyDistribution.png
│       ├── network_summary.txt
│       ├── graph_results.csv
│       └── graph_results_report.html
└── output_gen/                          # Genome-based analysis outputs
    ├── food_item_kos.csv
    ├── food_compound_report.html
    ├── microbe_compound_report.html     # only if --include-orgs and --n-weights
    ├── org_KO/
    │   ├── <one .txt file per food item>
    │   └── joined.txt
    ├── AMON_output/
    │   ├── AMON_log.txt
    │   ├── gene_set_1_enrichment.tsv
    │   ├── gene_set_2_enrichment.tsv
    │   ├── kegg_mapper.tsv
    │   ├── origin_table.tsv
    │   ├── enrichment_heatmap.png
    │   ├── venn.png
    │   ├── co_dict.json
    │   ├── ko_dict.json
    │   └── rn_dict.json
    └── graph/
        ├── WG_nodes_df.csv
        ├── WG_edges_df.csv
        ├── WG_AbundanceDistribution.png
        ├── WG_FoodFrequencyDistribution.png
        ├── network_summary.txt
        ├── graph_results.csv
        └── graph_results_report.html

Key Output Files

File	Description
run_info.txt	Pipeline version, run date, and full config used for this run
food_compound_report.html	Compounds identified in each food item
microbe_compound_report.html	Compounds predicted to be produced by microbes
graph_results_report.html	Network pattern analysis report with Neo4j query results
network_summary.txt	Summary statistics of the constructed network
graph_results.csv	Raw graph analysis results
*_nodes_df.csv	Node dataframe with optional frequency weights
*_edges_df.csv	Edge dataframe with optional abundance weights
*_AbundanceDistribution.png	Histogram of edge weights (requires --e-weights)
*_FoodFrequencyDistribution.png	Histogram of node weights (requires --n-weights)

Note

microbe_compound_report.html is only generated when both --include-orgs and --n-weights are specified.