weird variant TSV output

[Norina28]

Describe the bug
Hello,
I have a weird variant TSV output when I provide the gff file with a reference with multiple contigs. More or less each variant is duplicate/triplicate with the same values except the annotation columns( GFF_FEATURE, REF_CODON, REF_AA, ALT_CODON, ALT_AA). And when I go to search the GFF features, they belong to other contigs, the only thing it matches is the nt number. For example pos 30 of contig1, I get the gff features of pos 30 of other contigs.

To Reproduce
this is the command I ran:
samtools mpileup -aa -A -d 0 -B -Q 0 --reference MRSN599975.fasta MRSN599975negative_sort.bam | ivar variants -p MRSN599975negative -r MRSN599975.fasta -g annot.gff

Expected behavior
If I ran the variant without gff file everything is fine.

Screenshots

Thank you!

[Norina28]

Does anyone have any idea why it is happening?