Can diamond prepdb be used to make a taxonomically aware database?
0
1
Entering edit mode
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
ADD COMMENT
0
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.

ADD REPLY

Login before adding your answer.

Traffic: 1440 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6