I'm using this command (excuse the duplicate naming, I know it's bad form):
blastn -query cm-seqs/combined_seqs.fna -db combined_seqs.fna -out cm-matched.txt -num_alignments 1 -outfmt 10
to take a set of fasta sequences to blast against another data base I built with blast.
My query file has 4,364,417 sequences. The files resulting from the above command spat out 4,362,639 results. The difference is about 1800. Is this due to poor alignments for some sequences that didn't pass any of blasts default parameters? I assumed the result would be 1 "best" match in the database for each query sequence.