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.