converting to GTF3 ******************************************************************************** * - Start parsing - * ******************************************************************************** -------------------------- parse options and metadata -------------------------- => Accessing the feature level json files Using standard /home/sam/programs/miniforge3-24.7.1-0/envs/agat_env/lib/site_perl/5.26.2/auto/share/dist/AGAT/features_level1.json file Using standard /home/sam/programs/miniforge3-24.7.1-0/envs/agat_env/lib/site_perl/5.26.2/auto/share/dist/AGAT/features_level2.json file Using standard /home/sam/programs/miniforge3-24.7.1-0/envs/agat_env/lib/site_perl/5.26.2/auto/share/dist/AGAT/features_level3.json file Using standard /home/sam/programs/miniforge3-24.7.1-0/envs/agat_env/lib/site_perl/5.26.2/auto/share/dist/AGAT/features_spread.json file => Attribute used to group features when no Parent/ID relationship exists: * locus_tag * gene_id => merge_loci option deactivated => Accessing Ontology No ontology accessible from the gff file header! We use the SOFA ontology distributed with AGAT: /home/sam/programs/miniforge3-24.7.1-0/envs/agat_env/lib/site_perl/5.26.2/auto/share/dist/AGAT/so.obo Read ontology /home/sam/programs/miniforge3-24.7.1-0/envs/agat_env/lib/site_perl/5.26.2/auto/share/dist/AGAT/so.obo: 4 root terms, and 2472 total terms, and 1436 leaf terms Filtering ontology: We found 1757 terms that are sequence_feature or is_a child of it. -------------------------------- parse features -------------------------------- => GFF parser version used: 3 ******************************************************************************** * - End parsing - * * done in 109 seconds * ******************************************************************************** ******************************************************************************** * - Start checks - * ******************************************************************************** ---------------------------- Check1: feature types ----------------------------- ----------------------------------- ontology ----------------------------------- All feature types in agreement with the Ontology. ------------------------------------- agat ------------------------------------- AGAT can deal with all the encountered feature types (3rd column) ------------------------------ done in 0 seconds ------------------------------- ------------------------------ Check2: duplicates ------------------------------ None found ------------------------------ done in 0 seconds ------------------------------- -------------------------- Check3: sequential bucket --------------------------- Nothing to check as sequential bucket! ------------------------------ done in 0 seconds ------------------------------- --------------------------- Check4: l2 linked to l3 ---------------------------- No problem found ------------------------------ done in 0 seconds ------------------------------- --------------------------- Check5: l1 linked to l2 ---------------------------- No problem found ------------------------------ done in 0 seconds ------------------------------- --------------------------- Check6: remove orphan l1 --------------------------- We remove only those not supposed to be orphan None found ------------------------------ done in 1 seconds ------------------------------- ------------------------------ Check7: check cds ------------------------------- No problem found ------------------------------ done in 0 seconds ------------------------------- ----------------------------- Check8: check exons ------------------------------ No exons created No exons locations modified 10475 exons removed that were supernumerary No level2 locations modified ------------------------------ done in 11 seconds ------------------------------ ------------------------------ Check9: check utrs ------------------------------ No UTRs created No UTRs locations modified No supernumerary UTRs removed ------------------------------ done in 6 seconds ------------------------------- ------------------------ Check10: all level2 locations ------------------------- No problem found ------------------------------ done in 5 seconds ------------------------------- ------------------------ Check11: all level1 locations ------------------------- No problem found ------------------------------ done in 1 seconds ------------------------------- ---------------------- Check12: remove identical isoforms ---------------------- None found ------------------------------ done in 0 seconds ------------------------------- ******************************************************************************** * - End checks - * * done in 24 seconds * ******************************************************************************** => OmniscientI total time: 133 seconds Bye Bye