blastdbcmd: BLAST Database error: No alias or index file found for nucleotide database

[polinanvkv]

Expected Behavior

I want to create seqTaxDB with the downloaded nt database

Current Behavior

While augmenting the database with taxonomic information there's an error with BLAST+'s blastdbcmd

Steps to Reproduce (for bugs)

These steps go well:

wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
mkdir taxonomy && tar -xxvf taxdump.tar.gz -C taxonomy

The next command blastdbcmd -db nt -entry all > nt.fna returns an error BLAST Database error: No alias or index file found for nucleotide database [/scratch/users/pnovikova/refinement/taxonomy/mmseqs2/NT/nt] in search path [/mnt/lscratch/users/pnovikova/refinement/taxonomy/mmseqs2/NT:/mnt/lscratch/users/pnovikova/refinement/taxonomy/mmseqs2/NT:]

Context

Providing context helps us come up with a solution and improve our documentation for the future. blastdbcmd: 2.11.0+ Package: blast 2.11.0, build Oct 6 2020 03:24:05

Your Environment

Include as many relevant details about the environment you experienced the bug in.

• Which MMseqs version was used (Statically-compiled, self-compiled, Homebrew, etc.): bioconda, MMseqs2 Version: 12.113e3

[milot-mirdita]

I think you have to download the NT first (e.g. with BLAST's update_blastdb.pl) and then you can theoretically use blastdbcmd for the remaining commands.

However, I am not sure if the procedure described in the wiki still works with NCBI's recent change to the V5 database format. As far as I remember, it shouldn't work anymore. You might still be able to download the V4 format BLAST NT with update_blastdb.pl.

By the way, the new algorithm described in the preprint currently only works against protein databases. The search against nucleotide databases (such as the NT) still uses the older slower algorithm.

[nvpatin]

Was this issue ever resolved? I am getting the same error trying to build a database using blastdbcmd with NCBI nr.