Prepping and making a BLAST DB

[benfulton]

We've got an NCBI protein database set up, so it's in the form nr.00.ppi, nr.00.psq, nr.01.psq, nr.01.psq, etc. up to nr.69.psq. To use diamond, we've prepped the database with the command

diamond prepdb -d nr

Looks like this creates a set of ACC files, one for each nr index. But now, how do I make a database using these files? I tried

diamond makedb --in nr --db nr.dmnd --taxonmap prot.accession2taxid.FULL.gz --taxonnodes nodes.dmp --taxonnames names.dmp

but it thinks that nr is the name of a file here.

[bbuchfink]

makedb is for building a database from a fasta file. If you use prepdb on a blast db you can then directly use it with diamond, without running makedb.

[benfulton]

How do I get this to work? I tried

$ echo $BLASTDB
/N/soft/blastdb

$ ls $BLASTDB/nr.00*
/N/soft/blastdb/nr.00.acc  /N/soft/blastdb/nr.00.pog	 /N/soft/blastdb/nr.00.tar.gz.extracted
/N/soft/blastdb/nr.00.phd  /N/soft/blastdb/nr.00.ppd	 /N/soft/blastdb/nr.00.tar.gz.md5
/N/soft/blastdb/nr.00.phi  /N/soft/blastdb/nr.00.ppi	 /N/soft/blastdb/nr.00.tar.gz.md5receipt
/N/soft/blastdb/nr.00.phr  /N/soft/blastdb/nr.00.psq
/N/soft/blastdb/nr.00.pin  /N/soft/blastdb/nr.00.tar.gz

$ diamond blastp --in SBFOOD.faa -d nr -e 1e-12 --more-sensitive --threads 24 -f 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore stitle staxids sskingdoms -o test_diamond
diamond v2.0.13.151 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 24
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: 
#Target sequences to report alignments for: 25
Opening the database... No such file or directory
 [0.001s]
Error: Error calling stat on file nr

[bbuchfink]

Diamond does not read the BLASTDB environment variable. You have to specify the full path to the database.