------------------------------------------------------------------------------- This script is being run by perl v5.26.2 Bioperl location being used: /usr/local/lib/site_perl/5.26.2/Bio/ ------------------------------------------------------------------------------- => parse option and metadata: Accessing the feature level files: Using standard /usr/local/lib/site_perl/5.26.2/auto/share/dist/AGAT/features_level1.json file Using standard /usr/local/lib/site_perl/5.26.2/auto/share/dist/AGAT/features_level2.json file Using standard /usr/local/lib/site_perl/5.26.2/auto/share/dist/AGAT/features_level3.json file Using standard /usr/local/lib/site_perl/5.26.2/auto/share/dist/AGAT/features_spread.json file merge_locus option deactivated Accessing Ontology No ontology accessible from gff file header We will use the SOFA ontology distributed with AGAT: /usr/local/lib/site_perl/5.26.2/auto/share/dist/AGAT/sofa_2_5_3.obo read ontology /usr/local/lib/site_perl/5.26.2/auto/share/dist/AGAT/sofa_2_5_3.obo with 1 root terms, and 251 total terms, and 129 leaf terms => start parsing: GFF version parser used: 2 done in 0 seconds => report duplicates: none found. done in 0 seconds ****************************************************** * - Start extra check - * ****************************************************** ********************************** * Check1: _check_sequential * ********************************** done in 0 seconds ********************************** * Check2: _check_l2_linked_to_l3 * ********************************** done in 0 seconds ********************************** * Check3: _check_l1_linked_to_l2 * ********************************** done in 0 seconds ********************************** * Check4: _remove_orphan_l1 * ********************************** We removed 10 level1 features that had no subfeature linked to it. done in 0 seconds ********************************** * Check5: _check_exons * ********************************** done in 0 seconds ********************************** * Check6: _check_utrs * ********************************** done in 0 seconds ********************************** * Check7: _check_all_level2_posi * ********************************** done in 0 seconds ********************************** * Check8: _check_all_level1_posi * ********************************** done in 0 seconds ********************************** * Check10: _check_identical_isof * ********************************** done in 0 seconds ****************************************************** * - End extra check - * * done in 0 seconds * ****************************************************** => OmniscientI total time: 0 seconds GFF3 file parsed ##gff-version 3 usage: /usr/local/bin/agat_sp_gxf_to_gff3.pl -g test2.gtf Job done in 0 seconds