Output files and folders description for IdentifySpuriousGenes module

For –run-mode schema:

**OutputFolderName**
    The folder where the output files are stored.

1_schema_processing
    Folder containing schema processing results.

    master_nucleotide.fasta
        Master FASTA file.

    schema
        Folder containing schema files.

        loci_x.fasta
            FASTA file for locus x.

        new_loci_y.fasta
            FASTA file for new locus y.

        ...
            Other loci files.

        short
            Folder containing short loci files.

            loci_x.fasta
                Short FASTA file for locus x.

            new_loci_y.fasta
                Short FASTA file for new locus y.

            ...
                Other short loci files.

    schema_translation_folder
        Folder containing schema translations.

        loci_x.fasta
            Translation for locus x.

        new_loci_y.fasta
            Translation for new locus y.

        ...
            Other translations.

2_BLAST_processing
    Folder containing BLAST processing results.

    1_BLASTn_processing
        Folder containing BLASTn processing results.

        blast_db_nucl
            Folder containing BLASTn database.

            Blast_db_nucleotide.ndb
                BLASTn nucleotide database file.

            Blast_db_nucleotide.nhr
                BLASTn nucleotide header file.

            Blast_db_nucleotide.nin
                BLASTn nucleotide index file.

            Blast_db_nucleotide.nog
                BLASTn nucleotide organism group file.

            Blast_db_nucleotide.nsd
                BLASTn nucleotide sequence data file.

            Blast_db_nucleotide.nsi
                BLASTn nucleotide sequence index file.

            Blast_db_nucleotide.nsq
                BLASTn nucleotide sequence query file.

            Blast_db_nucleotide.ntf
                BLASTn nucleotide taxonomy file.

            Blast_db_nucleotide.nto
                BLASTn nucleotide taxonomy organism file.

        BLASTn_results
            Folder containing BLASTn results.

            blast_results_x.tsv
                BLASTn results for x.

            blast_results_y.tsv
                BLASTn results for y.

            ...
                Other BLASTn results.

    2_BLASTp_processing
        Folder containing BLASTp processing results.

        blastn_results_matches_translations
            Folder containing BLASTn results matches translations.

            cluster_rep_translation
                Folder containing BLASTn results of representative matches translations.

                cluster_matches_translation_x.tsv
                    Cluster representatives matches translation for x.

                cluster_matches_translation_y.tsv
                    Cluster representatives matches translation for y.

                ...
                    Other cluster representatives matches translations.

            cluster_matches_translation_x.tsv
                Cluster matches translation for x.

            cluster_matches_translation_y.tsv
                Cluster matches translation for y.

            ...
                Other cluster matches translations.

        BLASTp_results
            Folder containing BLASTp results.

            blast_results_x.tsv
                BLASTp results for x.

            blast_results_y.tsv
                BLASTp results for y.

            ...
                Other BLASTp results.

        BLASTp_results_self_score_results
            Folder containing BLASTp self-score results.

            blast_results_x.tsv
                BLASTp self-score results for x.

            blast_results_y.tsv
                BLASTp self-score results for y.

            ...
                Other BLASTp self-score results.

3_processing_results
    Folder containing processing results.

    blast_results
        Folder containing BLAST results.

        blast_all_matches.tsv
            TSV file containing all BLAST matches.

        blast_by_cluster
            Folder containing BLAST results by cluster.

            blast_joined_cluster_x.tsv
                BLAST results for cluster x.

            blast_retained_y.tsv
                BLAST results for cluster y.

            ...
                Other cluster results.

        blast_results_by_class
            Folder containing BLAST results by class.

            class_1a.tsv
                BLAST results for class 1.

            class_2a.tsv
                BLAST results for class 2.

            ...
                Other class results.

    **count_results_by_cluster.tsv**
        TSV file containing count results by cluster.

    **drop_loci_reason.tsv**
        TSV file containing reasons for dropping loci.

    **recommendations.tsv**
        TSV file containing recommendations.

    **recommendations_annotations.tsv**
        TSV file containing the annotations of the recommendations loci.

    **related_matches.tsv**
        TSV file containing related matches.

For –run-mode unclassified_cds:

**OutputFolderName**
    The folder where the output files are stored.

1_CDS_processing
    Folder containing CDS processing results.

    CDS_not_found.fasta
        FASTA file containing CDS not found.

    CDS_not_found_translation.fasta
        FASTA file containing translations of CDS not found.

2_BLAST_processing
    Folder containing BLAST processing results.

    1_BLASTn_processing
        Folder containing BLASTn processing results.

        blast_db_nucl
            Folder containing BLASTn database.

            Blast_db_nucleotide.ndb
                BLASTn nucleotide database file.

            Blast_db_nucleotide.nhr
                BLASTn nucleotide header file.

            Blast_db_nucleotide.nin
                BLASTn nucleotide index file.

            Blast_db_nucleotide.nog
                BLASTn nucleotide organism group file.

            Blast_db_nucleotide.nsd
                BLASTn nucleotide sequence data file.

            Blast_db_nucleotide.nsi
                BLASTn nucleotide sequence index file.

            Blast_db_nucleotide.nsq
                BLASTn nucleotide sequence query file.

            Blast_db_nucleotide.ntf
                BLASTn nucleotide taxonomy file.

            Blast_db_nucleotide.nto
                BLASTn nucleotide taxonomy organism file.

        BLASTn_results
            Folder containing BLASTn results.

            blast_results_x.tsv
                BLASTn results for x.

            blast_results_y.tsv
                BLASTn results for y.

            ...
                Other BLASTn results.

    2_BLASTp_processing
        Folder containing BLASTp processing results.

        blastn_results_matches_translations
            Folder containing BLASTn results matches translations.

            cluster_rep_translation
                Folder containing BLASTn results of representative matches translations.

                cluster_matches_translation_x.tsv
                    Cluster representatives matches translation for x.

                cluster_matches_translation_y.tsv
                    Cluster representatives matches translation for y.

                ...
                    Other cluster representatives matches translations.

            cluster_matches_translation_x.tsv
                Cluster matches translation for x.

            cluster_matches_translation_y.tsv
                Cluster matches translation for y.

            ...
                Other cluster matches translations.

        BLASTp_results
            Folder containing BLASTp results.

            blast_results_x.tsv
                BLASTp results for x.

            blast_results_y.tsv
                BLASTp results for y.

            ...
                Other BLASTp results.

        BLASTp_results_self_score_results
            Folder containing BLASTp self-score results.

            blast_results_x.tsv
                BLASTp self-score results for x.

            blast_results_y.tsv
                BLASTp self-score results for y.

            ...
                Other BLASTp self-score results.

3_processing_results
    Folder containing processing results.

    blast_results
        Folder containing BLAST results.

        blast_all_matches.tsv
            TSV file containing all BLAST matches.

        blast_by_cluster
            Folder containing BLAST results by cluster.

            blast_joined_cluster_x.tsv
                BLAST results for cluster x.

            blast_retained_y.tsv
                BLAST results for cluster y.

            ...
                Other cluster results.

        blast_results_by_class
            Folder containing BLAST results by class.

            class_1a.tsv
                BLAST results for class 1.

            class_2a.tsv
                BLAST results for class 2.

            ...
                Other class results.

    cds_id_changes.tsv
        TSV file containing changes in CDS IDs.

    dropped_cds.tsv
        TSV file containing dropped CDS.

    Graph_folder
        Folder containing graphs.

        All_of_CDS_graphs.html
            HTML file containing all CDS graphs.

        graphs_class_1a.html
            HTML file containing class 1a graphs.

        ...
            Other graph files.

    **count_results_by_cluster.tsv**
        TSV file containing count results by cluster.

    **drop_loci_reason.tsv**
        TSV file containing reasons for dropping loci.

    **recommendations.tsv**
        TSV file containing recommendations.

    **recommendations_annoations.tsv**
        TSV file containing the annotations of the recommendations loci.

    **related_matches.tsv**
        TSV file containing related matches.

    **temp_fastas**
        Folder containing temporary FASTA files.

        **cluster_x.fasta**
            Temporary FASTA file for cluster x.

        **cluster_y.fasta**
            Temporary FASTA file for cluster y.

        **...**
            Other temporary FASTA files.