Can diamond prepdb be used to make a taxonomically aware database?
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5 weeks ago
cedric.blais ▴ 10

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?

blast diamond taxonomy • 206 views
Entering edit mode

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 of diamond can use NCBI's preformatted blast databases as is.


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