I am trying to run the following gffcompare command:
gffcompare -r ref.gff -G -o merged stringtie-merged.gtf
ref.gff - downloaded from NCBI
string-merged.gtf - obtained from stringtie --merge
command
Error encountered : GFF Error: overlapping duplicate transcript feature (ID=gene29892)
When I grep "gene29892" from both the ref.gff and stringtie-merged.gtf
From ref.gff
NC_007957.1 RefSeq gene 74631 74744 . + . ID=gene29892;Dbxref=GeneID:4025012;Name=rps12;exception=trans-splicing;gbkey=Gene;gene=rps12;gene_biotype=protein_coding;locus_tag=ViviCp045;part=1/2
NC_007957.1 RefSeq gene 146276 147073 . + . ID=gene29892;Dbxref=GeneID:4025012;Name=rps12;exception=trans-splicing;gbkey=Gene;gene=rps12;gene_biotype=protein_coding;locus_tag=ViviCp045;part=2/2
NC_007957.1 RefSeq CDS 74631 74744 . + 0 ID=cds41168;Parent=gene29892;Dbxref=Genbank:YP_567100.1,GeneID:4025012;Name=YP_567100.1;exception=trans-splicing;gbkey=CDS;gene=rps12;product=ribosomal protein S12;protein_id=YP_567100.1;transl_table=11
NC_007957.1 RefSeq CDS 146276 146507 . + 0 ID=cds41168;Parent=gene29892;Dbxref=Genbank:YP_567100.1,GeneID:4025012;Name=YP_567100.1;exception=trans-splicing;gbkey=CDS;gene=rps12;product=ribosomal protein S12;protein_id=YP_567100.1;transl_table=11
NC_007957.1 RefSeq CDS 147048 147073 . + 2 ID=cds41168;Parent=gene29892;Dbxref=Genbank:YP_567100.1,GeneID:4025012;Name=YP_567100.1;exception=trans-splicing;gbkey=CDS;gene=rps12;product=ribosomal protein S12;protein_id=YP_567100.1;transl_table=11
NC_007957.1 RefSeq exon 146276 146507 . + . ID=id318095;Parent=gene29892;Dbxref=GeneID:4025012;exon_number=1;gbkey=exon;gene=rps12
NC_007957.1 RefSeq exon 147048 147073 . + . ID=id318096;Parent=gene29892;Dbxref=GeneID:4025012;exon_number=2;gbkey=exon;gene=rps12
From stringtie-merged.gtf
NC_007957.1 StringTie transcript 74631 147073 1000 + . gene_id "MSTRG.117"; transcript_id "gene29892"; gene_name "rps12"; ref_gene_id "gene29892";
NC_007957.1 StringTie exon 74631 74744 1000 + . gene_id "MSTRG.117"; transcript_id "gene29892"; exon_number "1"; gene_name "rps12"; ref_gene_id "gene29892";
NC_007957.1 StringTie exon 146276 146507 1000 + . gene_id "MSTRG.117"; transcript_id "gene29892"; exon_number "2"; gene_name "rps12"; ref_gene_id "gene29892";
NC_007957.1 StringTie exon 147048 147073 1000 + . gene_id "MSTRG.117"; transcript_id "gene29892"; exon_number "3"; gene_name "rps12"; ref_gene_id "gene29892";
NC_007957.1 StringTie transcript 146276 147073 1000 + . gene_id "MSTRG.117"; transcript_id "gene29892"; gene_name "rps12"; ref_gene_id "gene29892";
NC_007957.1 StringTie exon 146276 147073 1000 + . gene_id "MSTRG.117"; transcript_id "gene29892"; exon_number "1"; gene_name "rps12"; ref_gene_id "gene29892";
What could be possibly wrong as I cannot see any duplicate values! There are identical "starts" "stops" but the tags/labels are different.