format issue with gff files

[khemlalnirmalkar]

Hi, I am a newbie to assembly-annotation work and recently i needed to run prokka twice for the same sets of samples but found a different head for gff files

1. head of gff from first time
   ##gff-version 3 ##sequence-region NODE_1_length_1061053_cov_8.413562 1 1061053 ##sequence-region NODE_2_length_715344_cov_5.218381 1 715344

2. head of gff from second run of same sample ##gff-version 3 ##sequence-region gnl|X|CGFCCPGG_1 1 1061053 ##sequence-region gnl|X|CGFCCPGG_2 1 715344

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I need the format like my first run Please may i know why its different? both times my script was the same prokka ${i}scaffolds.fasta --outdir prokka${i} --centre X --compliant --norrna --notrna --metagenome --cpus $(nproc)

Thanks, Khem