Blast database formatted with prepdb does not support taxonomic information

[cedricblais]

Hello,

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?

Thank you!

[riksub]

I have the same problem.
Nr database was already installed in the server and it was prepared with prepdb (v. 2.1.9).
Any idea why is not working?

[bbuchfink]

The feature is not supported but I plan to implement it.

[riksub]

The feature is not supported but I plan to implement it.

I see. What do you think is the best way to build the diamond database from a downloaded nr to have taxonomy features?
And how much storage do you think the resulting diamond db could occupy?

I am asking since I have no root access on the cluster to download the db as fasta and format it with diamond makedb for the moment and I have to provide details to the cluster admin.