"intron/exon"" Features locations are duplicated - consider merging qualifiers, unable to remove it.

[kumariindu-commits]

Is your feature request related to a problem? Please describe.
When validating embl file, the following error is faced: 1091,"ERROR: ""exon"" Features locations are duplicated - consider merging qualifiers. [ line: 1091 of Cp.embl.gz, line: 1003 of Cp.embl.gz]",ATGAAAACCT AAATTCATTT AGGGCCGAAA CTGATGCTGA TTTTCTGGAA AGGTTTAAGC 61740,locus_tag not found,Not found,Not found,NA,NA,NA,NA,Unmatched format. Features merging, removal of duplicate of intron and exon has been tried but same error is coming. I have tried to use agat_sp_fix_features_locations_duplicated.pl and agat_convert_sp_gxf2gxf.pl (earlier file: Chr1 AUGUSTUS gene 5596 9684 . + . ID=Gene00001; protein ZIOFF_070466;Ontology_term=nucleic acid binding,RNA-DNA hybrid ribonuclease activity;Ontology_id=GO:0003676,GO:0004523 Chr1 AUGUSTUS mRNA 5596 9684 0.68 + . ID=Gene00001;Parent=Gene00001; Chr1 AUGUSTUS start_codon 5596 5598 . + 0 ID=Gene00001;Parent=Gene00001; Chr1 AUGUSTUS CDS 5596 9684 0.68 + 0 ID=Gene00001;Parent=Gene00001; Chr1 AUGUSTUS exon 5596 9684 . + . ID=Gene00001;Parent=Gene00001; Chr1 AUGUSTUS stop_codon 9682 9684 . + 0 ID=Gene00001;Parent=Gene00001; Chr1 AUGUSTUS gene 40238 45035 . - . ID=Gene00002; protein LOC105179067 isoform X1 Chr1 AUGUSTUS mRNA 40238 45035 0.09 - . ID=Gene00002;Parent=Gene00002; Chr1 AUGUSTUS stop_codon 40238 40240 . - 0 ID=Gene00002;Parent=Gene00002; and after running the command files is like this: after removing duplicate Chr1 AUGUSTUS start_codon 5596 5598 . + 0 ID=Gene00001;Parent=Gene00001 Chr1 AUGUSTUS gene 5596 9684 . + . ID=Gene00001;Parent=.;protein ZIOFF_070466;Ontology_term=nucleic acid binding,RNA-DNA hybrid ribonuclease activity;Ontology_id=GO:0003676,GO:0004523 Chr1 AUGUSTUS mRNA 5596 9684 0.68 + . ID=Gene00001;Parent=Gene00001 Chr1 AUGUSTUS CDS 5596 9684 0.68 + 0 ID=Gene00001;Parent=Gene00001 Chr1 AUGUSTUS exon 5596 9684 . + . ID=Gene00001;Parent=Gene00001 Chr1 AUGUSTUS stop_codon 9682 9684 . + 0 ID=Gene00001;Parent=Gene00001 Chr1 AUGUSTUS stop_codon 40238 40240 . - 0 ID=Gene00002;Parent=Gene00002 Chr1 AUGUSTUS CDS 40238 40337 0.87 - 1 ID=Gene00002;Parent=Gene00002 Chr1 AUGUSTUS exon 40238 40337 . - . ID=Gene00002;Parent=Gene00002, utilities of AGAT. In addition to this I have tried to remove duplicate features removal and merge by scripts also but its not working. Please suggest how to solve it?

[Juke34]

Skipping exons should fix the issue. They are useless to submit because contained in the mRNA information made by EMBLmyGFF3.
To get rid of them follow instructions here: https://github.com/NBISweden/EMBLmyGFF3?tab=readme-ov-file#feature-type