gt gff3 loss of intergenic regions

[edinatale]

I am interested in adding introns in my genome annotation mygenome.gff3.
After running the command below, I obtain an output genome_with_introns.gff3 in which there is no "intergenic_region" annotation anymore.
Is there something I'm not considering, that would help me solving this issue?

mygenome.gff3

##gff-version 3
##sequence-region chr_00 1 18946431
chr_00	assembly	sequence_assembly	1	18946431	.	+	.	ID=chr_00;Ontology_term=SO:0000353
chr_00	ORCAE	intergenic_region	1	149	.	.	.	ID=inter:first;Name=first;Ontology_term=SO:0000605
chr_00	ORCAE	gene	150	6731	.	-	.	ID=Ec-00_000010;Name=Ec-00_000010;Alias=Esi_1000_0001,Esi1000_0001;length=6582
chr_00	ORCAE	mRNA	150	6731	.	-	.	ID=Ec-00_000010.1;Parent=Ec-00_000010;gene_id=Ec-00_000010.1;Name=Ec-00_000010.1;Alias=Esi_1000_0001,Esi1000_0001;length=1971
chr_00	ORCAE	exon	150	428	.	-	.	ID=Ec-00_000010.1.10;Parent=Ec-00_000010.1;gene_id=Ec-00_000010.1;Ontology_term=SO:0000202
chr_00	ORCAE	exon	898	1100	.	-	.	ID=Ec-00_000010.1.9;Parent=Ec-00_000010.1;gene_id=Ec-00_000010.1;Ontology_term=SO:0000004
chr_00	ORCAE	exon	1536	1674	.	-	.	ID=Ec-00_000010.1.8;Parent=Ec-00_000010.1;gene_id=Ec-00_000010.1;Ontology_term=SO:0000004
chr_00	ORCAE	exon	2092	2268	.	-	.	ID=Ec-00_000010.1.7;Parent=Ec-00_000010.1;gene_id=Ec-00_000010.1;Ontology_term=SO:0000004

my command

gt gff3 -retainids -addintrons my_genome.gff3  > my_genome_with_introns.gff3

genome_with_introns.gff3

chr_00  ORCAE   gene    150     6731    .       -       .       ID=Ec-00_000010;Name=Ec-00_000010;Alias=Esi_1000_0001,Esi1000_0001;length=6582
chr_00  ORCAE   mRNA    150     6731    .       -       .       ID=Ec-00_000010.1;Parent=Ec-00_000010;gene_id=Ec-00_000010.1;Name=Ec-00_000010.1;Alias=Esi_1000_0001,Esi1000_0001;length=1971
chr_00  ORCAE   exon    150     428     .       -       .       ID=Ec-00_000010.1.10;Parent=Ec-00_000010.1;gene_id=Ec-00_000010.1;Ontology_term=SO:0000202
chr_00  ORCAE   CDS     150     428     .       -       0       ID=CDS:Ec-00_000010.1;Parent=Ec-00_000010.1;gene_id=Ec-00_000010.1;Name=Ec-00_000010.1;Ontology_term=SO:0000202
chr_00  .       intron  429     897     .       -       .       Parent=Ec-00_000010.1
chr_00  ORCAE   exon    898     1100    .       -       .       ID=Ec-00_000010.1.9;Parent=Ec-00_000010.1;gene_id=Ec-00_000010.1;Ontology_term=SO:0000004
chr_00  ORCAE   CDS     898     1100    .       -       2       ID=CDS:Ec-00_000010.1;Parent=Ec-00_000010.1;gene_id=Ec-00_000010.1;Name=Ec-00_000010.1;Ontology_term=SO:0000004
chr_00  .       intron  1101    1535    .       -       .       Parent=Ec-00_000010.1
chr_00  ORCAE   exon    1536    1674    .       -       .       ID=Ec-00_000010.1.8;Parent=Ec-00_000010.1;gene_id=Ec-00_000010.1;Ontology_term=SO:0000004

gt -version 1.6.1
Linux x86_64

[satta]

Unfortunately I can not reproduce this:

$ gt -version | head -n 1
gt (GenomeTools) 1.6.1
$ cat test1022.gff3 
##gff-version 3
##sequence-region chr_00 1 18946431
chr_00	assembly	sequence_assembly	1	18946431	.	+	.	ID=chr_00;Ontology_term=SO:0000353
chr_00	ORCAE	intergenic_region	1	149	.	.	.	ID=inter:first;Name=first;Ontology_term=SO:0000605
chr_00	ORCAE	gene	150	6731	.	-	.	ID=Ec-00_000010;Name=Ec-00_000010;Alias=Esi_1000_0001,Esi1000_0001;length=6582
chr_00	ORCAE	mRNA	150	6731	.	-	.	ID=Ec-00_000010.1;Parent=Ec-00_000010;gene_id=Ec-00_000010.1;Name=Ec-00_000010.1;Alias=Esi_1000_0001,Esi1000_0001;length=1971
chr_00	ORCAE	exon	150	428	.	-	.	ID=Ec-00_000010.1.10;Parent=Ec-00_000010.1;gene_id=Ec-00_000010.1;Ontology_term=SO:0000202
chr_00	ORCAE	exon	898	1100	.	-	.	ID=Ec-00_000010.1.9;Parent=Ec-00_000010.1;gene_id=Ec-00_000010.1;Ontology_term=SO:0000004
chr_00	ORCAE	exon	1536	1674	.	-	.	ID=Ec-00_000010.1.8;Parent=Ec-00_000010.1;gene_id=Ec-00_000010.1;Ontology_term=SO:0000004
chr_00	ORCAE	exon	2092	2268	.	-	.	ID=Ec-00_000010.1.7;Parent=Ec-00_000010.1;gene_id=Ec-00_000010.1;Ontology_term=SO:0000004
$ gt gff3 -retainids -addintrons test1022.gff3 > test1022_with_introns.gff3
$ cat test1022_with_introns.gff3
##gff-version 3
##sequence-region   chr_00 1 18946431
chr_00	assembly	sequence_assembly	1	18946431	.	+	.	ID=chr_00;Ontology_term=SO:0000353
###
chr_00	ORCAE	intergenic_region	1	149	.	.	.	ID=inter:first;Name=first;Ontology_term=SO:0000605
###
chr_00	ORCAE	gene	150	6731	.	-	.	ID=Ec-00_000010;Name=Ec-00_000010;Alias=Esi_1000_0001,Esi1000_0001;length=6582
chr_00	ORCAE	mRNA	150	6731	.	-	.	ID=Ec-00_000010.1;Parent=Ec-00_000010;gene_id=Ec-00_000010.1;Name=Ec-00_000010.1;Alias=Esi_1000_0001,Esi1000_0001;length=1971
chr_00	ORCAE	exon	150	428	.	-	.	ID=Ec-00_000010.1.10;Parent=Ec-00_000010.1;gene_id=Ec-00_000010.1;Ontology_term=SO:0000202
chr_00	.	intron	429	897	.	-	.	Parent=Ec-00_000010.1
chr_00	ORCAE	exon	898	1100	.	-	.	ID=Ec-00_000010.1.9;Parent=Ec-00_000010.1;gene_id=Ec-00_000010.1;Ontology_term=SO:0000004
chr_00	.	intron	1101	1535	.	-	.	Parent=Ec-00_000010.1
chr_00	ORCAE	exon	1536	1674	.	-	.	ID=Ec-00_000010.1.8;Parent=Ec-00_000010.1;gene_id=Ec-00_000010.1;Ontology_term=SO:0000004
chr_00	.	intron	1675	2091	.	-	.	Parent=Ec-00_000010.1
chr_00	ORCAE	exon	2092	2268	.	-	.	ID=Ec-00_000010.1.7;Parent=Ec-00_000010.1;gene_id=Ec-00_000010.1;Ontology_term=SO:0000004
###

As you can see, both the intergenic_region as well as assembly features are still there, which you are reporting missing in your output.

Your result GFF looks a little weird as well -- there is no ##sequence-region directive, for example, which GenomeTools always outputs. This does not look like direct GenomeTools output. Has the output been postprocessed in any way, e.g. piped through another tool?