Oftentimes, gff files are unsorted, with respect to the occurrence of features along the genome sequence. Some tool require, however, sorted gff files as input. This is how you sort them
You need to have the genome tools package installed
conda install bioconda::genometools-genometools
gt gff3 -sort -tidy YOURGFF.gff > YOURGFF_sorted.gff
The command assumes that your gff file is in gff3 format. Replace the 'YOURGFF.gff' with your actual filename