How does --iterate work with --max-target-seqs 1 ?

[Abieskawa]

Hello, I am using diamond blastp and database is the local configured NR (000-116) database. I use these commands:

diamond blastp --max-target-seqs 1 -e 1e-3 --threads 96 --query-cover 0.5 --iterate -q ${query_protein} -d ${NR} -o ${output.tsv}

--max-target-seqs is set as 1 because of the requirement of the downstream analysis. Does diamond look for the best one (--max-target-seqs 1 ) during the iteration? I am not sure how to interpret this command.

Thanks~

[bbuchfink]

--iterate will run multiple search rounds with increasing sensitivity. It will usually find the best hit for the query, but it will stop looking once a hit has been found. To have higher confidence in finding the best hit, you should run it without --iterate.