Output directory

Output directory structure

MicFunPred creates multiple directories and files. Each files are named and arranged properly in respective directories which is quite self-explanatory.

├── CAZymes_metagenome    # CAZymes
│   ├── CAZymes_metagenome.tsv.gz
│   └── CAZymes_metagenome_with_description.tsv.gz
├── COG_metagenome    # COG
│   ├── COG_metagenome.tsv.gz
│   └── COG_metagenome_with_description.tsv.gz
├── KO_metagenome   # KEGG
│   ├── KO_metagenome_minPath_pruned.txt    # KO metagenome prunned KO ids by MinPath
│   ├── KO_metagenome.tsv.gz    # Original predicted KO metagenome 
│   ├── KO_metagenome_with_description.tsv.gz   # KO metagenome with BRITE hierarchies
│   ├── minpath_in.ko # temporary file for MinPath
│   ├── minpath.out   # MinPath raw output
│   ├── summarized_by_A.tsv.gz    # KO metagenome summarized by A level hierarchy
│   ├── summarized_by_B.tsv.gz    # KO metagenome summarized by B level hierarchy
│   ├── summarized_by_C.tsv.gz    # KO metagenome summarized by C level hierarchy
│   └── summarized_by_Pathway_Module.tsv.gz   # KO metagenome summarized by Pathway Module hierarchy
├── MetaCyc_metagenome    # MetaCyc 
│   ├── EC_metagenome.tsv.gz    # EC metagenome
│   ├── minPath_files     # intermediate files generated by MinPath
│   │   ├── sample1_minpath_in.txt
│   │   ├── sample1_minpath.out
│   │   ├── sample1_minpath.out.details
│   │   ├── sample2_minpath_in.txt
│   │   ├── sample2_minpath.out
│   │   ├── sample2_minpath.out.details
│   │   ├── sample3_minpath_in.txt
│   │   ├── sample3_minpath.out
│   │   └── sample3_minpath.out.details
│   ├── PathwayAbundance.tsv.gz   # Pathway metagenome extracted from EC metagenome
│   ├── PathwayAbundance_with_names.tsv.gz    # Pathway metagenome with names
│   ├── Pathway_summarize_by_Types.tsv.gz   # Pathway metagenome summarized by MetaCyc types
│   └── RXN_metagenome.tsv.gz   # Reaction metagenome
├── out.blast   # BLAST output of OTU/ASV sequences and 16S rRNA database
├── Pfam_metagenome   # PFAM 
│   ├── Pfam_metagenome.tsv.gz    # PFAM metagenome
│   └── Pfam_metagenome_with_description.tsv.gz   # PFAM metagenome with names
├── predicted_16S_copy_numbers.txt    # predicted 16S rRNA copy numbers of each genra
├── predicted_CAZymes.tsv.gz    # predicted CAZymes copy number in each genera
├── predicted_COG.tsv.gz    # predicted COG copy number in each genera
├── predicted_EC.tsv.gz   # predicted EC copy number in each genera
├── predicted_KO.tsv.gz   # predicted KO copy number in each genera
├── predicted_Pfam.tsv.gz   # predicted PFAM copy number in each genera
├── predicted_TIGRFAM.tsv.gz    # predicted TIGRFAM copy number in each genera
├── tax_abund_normalized.table    # abundance table normalized
├── tax_abund.table   # abundance table
└── TIGRFAM_metagenome    # TIGRFAM
    ├── TIGRFAM_metagenome.tsv.gz   # TIGRFAM metagenome
    └── TIGRFAM_metagenome_with_description.tsv.gz    # TIGRFAM metagenome with names