agat_sp_manage_functional_annotation.pl

[okendojo]

I have interproscan.tsv, and I want to add the protein domains in the GFF file, agat_sp_manage_functional_annotation.pl does the job but I was wondering why column 4 and 5 are having duplicate coordinates. Is there a flag I should pass to fix this?

##gff-version 3
#!genome-build  GRCz12ab
#!genome-version GRCz12ab
#!genome-date 2025-08
#!genome-build-accession GCA_052040795.1
#!genebuild-last-updated 2025-12
1       GRCz12ab        region  1       62059388        .       .       .       ID=region:1;Alias=CM124807.1
1       .       biological_region       65866   66293   167     .       .       ID=agat-biological_region-110122;external_name=oe %3D 0.89;logic_name=cpg
1       .       biological_region       65866   66293   167     .       .       ID=agat-biological_region-110123;external_name=oe %3D 0.89;logic_name=cpg
1       .       biological_region       65866   66293   167     .       .       ID=agat-biological_region-110124;external_name=oe %3D 0.89;logic_name=cpg
1       .       biological_region       71844   72269   259     .       .       ID=agat-biological_region-110125;external_name=oe %3D 0.68;logic_name=cpg
1       .       biological_region       71844   72269   259     .       .       ID=agat-biological_region-110126;external_name=oe %3D 0.68;logic_name=cpg
1       .       biological_region       71844   72269   259     .       .       ID=agat-biological_region-110127;external_name=oe %3D 0.68;logic_name=cpg
1       .       biological_region       76466   77089   403     .       .       ID=agat-biological_region-110128;external_name=oe %3D 0.90;logic_name=cpg
1       .       biological_region       76466   77089   403     .       .       ID=agat-biological_region-110129;external_name=oe %3D 0.90;logic_name=cpg
1       .       biological_region       76466   77089   403     .       .       ID=agat-biological_region-110130;external_name=oe %3D 0.90;logic_name=cpg
1       .       biological_region       78056   78570   368     .       .       ID=agat-biological_region-110131;external_name=oe %3D 0.70;logic_name=cpg
1       .       biological_region       78056   78570   368     .       .       ID=agat-biological_region-110132;external_name=oe %3D 0.70;logic_name=cpg
1       .       biological_region       78056   78570   368     .       .       ID=agat-biological_region-110133;external_name=oe %3D 0.70;logic_name=cpg
1       .       biological_region       78345   78345   0.999   +       .       ID=agat-biological_region-110134;logic_name=eponine
1       .       biological_region       78345   78345   0.999   +       .       ID=agat-biological_region-110135;logic_name=eponine
1       .       biological_region       78345   78345   0.999   +       .       ID=agat-biological_region-110136;logic_name=eponine
1       .       biological_region       97700   98813   867     .       .       ID=agat-biological_region-110137;external_name=oe %3D 1.18;logic_name=cpg
1       .       biological_region       97700   98813   867     .       .       ID=agat-biological_region-110138;external_name=oe %3D 1.18;logic_name=cpg
1       .       biological_region       97700   98813   867     .       .       ID=agat-biological_region-110139;external_name=oe %3D 1.18;logic_name=cpg
1       .       biological_region       97940   97942   0.999   +       .       ID=agat-biological_region-110140;logic_name=eponine
1       .       biological_region       97940   97942   0.999   +       .       ID=agat-biological_region-110141;logic_name=eponine
1       .       biological_region       97940   97942   0.999   +       .       ID=agat-biological_region-110142;logic_name=eponine

[Juke34]

As they have uniq Identifier AGAT keep them. I guess they where described several times in the input file, AGAT probably added a uniq Identifier to each of them, and them keep all of them. You should check the input GFF file.

[okendojo]

The files I am working with are available here: https://ftp.ebi.ac.uk/pub/databases/ensembl/pre-release/Danio_rerio/GCA_052040795.1/ , could you have a look and advise?