I'm trying to blast a single sequence against a custom blastdb (7 Gb in size) and the number of results is lower than what I expected.
Also, if I remove the sequence that were correctly aligned and launch a second blastn against the truncated blastdb, I get new results.
I indexed the custom blastdb with the following command:
makeblastdb -in db.fna -dbtype nucl
Then I launched blastn with the following command:
blastn -db db.fna -max_target_seqs 1000000 -word_size 11 -outfmt 6 -query query.fna > blast.out
I tried those commands with blast v2.4.0 and v2.7.1 that are currently available on our servers.
Am I missing something?