Does Prokka or gff3 change the sequence / subject ID of fasta files? I used prokka to create a database for some fasta files but I noticed a strange difference between the prokka and fasta files. Normally the seqid for the gff3 output for prokka has seqid's that match the sequence id's of the fasta files. The files I just produced with prokka have a different seqid than my fasta files. My fasta files look like this 

&gt;NODE_108_length_645_cov_0.679537_ID_215


However the prokka output gff3 file for the same fasta file uses a seqid like this

gnl|X|JHIOGLGG_28


What would cause this difference? And do the last digits still correlate to the same seqid's even though the string before it has changed?
Prokka is an annotation tool. It takes your contigs file with fasta headers &gt;NODE_108...and searchs for ORFs and their putative functions. Prokka produces submission ready output, the new fasta headers you see &gt;JHIOGLGG_28...are locus tags and gene description from the annotation and are not related to contig node data. Please see the github information page for more info.