Why do BLASTn and prokka not seem to be searching the whole fasta file? When I use blastn and prokka (I will detail exactly how I did so below) on a 2.8 million bp fasta file I get output start/end numbers that do not seem to cover the entire genome. 

Starting with a .fna genome such as genome.fna I ...

1 - blastn

Searched the genome for 3135 different 28-mers using BLASTn.

makeblastdb -in genome.fna -dbtype nucl -parse_seqids -out ./output/genome


next command in python

blast_tsv = NcbiblastnCommandline(query=Q, db=DB, perc_identity=100, outfmt=6, out=(OUT))
    stdout, stderr = blast_tsv()


Q is this list of k-mers. DB is the database created

This outputs a list of search results but the important thing is that none of the start/end (columns 7 and 8) integers were greater than 100,000 yet the entire genome is 2.8 million base pairs long. I can provide the link to this file in the comments. Does this have to do with blastn stopping searching after finding one match? And if so how can I tell blastn to search for every match for each k-mer? (I'm open to using other blastn programs other than biopython)

2 - prokka

I used prokka to create gff files for the genome. 

prokka-1.12/bin/prokka —setupdb
prokka-1.12/bin/prokka -kingdom Bacteria -rfam -outdir ./prokka_database/genome -force -prefix "${genome/.fna/}" genome.fna


Th gff file produced by this command only described genes with start and end positions less than 200k. I can provide the link to this file as well.
With a k-mer size of 28 it shouldn't be finding that many matches. And the prokka results are suspicious as well. Maybe you have multiple contigs (none larger than 100kb) in that file? What is the result of 


grep ^'>' fasta_file | wc -l


? This would show how many contigs you have in the file.