# 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.

grep ^'>' fasta_file | wc -l