I have a local copy of the blast nr database, which I prepared for a diamond search with prepdb.
After running a search using the "staxids sskingdoms skingdoms sphylums sscinames" options for outfmt 6, I got the following error message:
Error: Taxonomy features are not supported for the BLAST database format.
Running a vanilla blast search against the blast database worked just fine, so I can guarantee that this isn't an issue with the blast database itself not being taxonomically aware.
From what I saw in the diamond documentation, in order to have taxonomy features you need to use --taxonmap when running makedb to create the diamond database, but there is no mention of prepdb. Is there any way to have taxonomically aware searches using a database formatted with prepdb?
Should be possible: How can I get taxonomy identifiers (staxids) using diamond? (Error: Invalid output format. Allowed values: 0,5,6,100,101,102)
Are you using an older version of
diamond? Latest versions ofdiamondcan use NCBI's preformatted blast databases as is.