Why do BLASTn and prokka not seem to be searching the whole fasta file?
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.