I am running blastx using the following command:
blastx -query CDS.fa -db local_path_nr -num_threads 36 -evalue 1e-5 -outfmt 6 -max_target_seqs 1 -out CDS_blast.txt
I aim to get one hit for each query only but there are still, say 2-3 hits, per query occasionally. How do I save the top hit only? I know this can be done post-blast, but can I simply achieve it while running blast? Thanks!