nr database "No alias or index file found for protein database"
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3.3 years ago
semans • 0

I am trying to create an nr database, from the nr files provided by NCBI, on a server to run some blast searches. Once I try to run the blast search, the following error is returned

blastp -query ngruberi_TTL1.fasta -db /home/sh17a/nr
BLAST Database error: No alias or index file found for protein database [/home/sh17a/nr] in search path [/home/sh17a::]


The nr directory contains the files from decompressing nr.112.tar.gz from ftp://ftp.ncbi.nlm.nih.gov/blast/db/, which yields the following:

nr.112.phd nr.112.phr nr.112.pnd nr.112.pog nr.112.ppi nr.112.psi taxdb.btd nr.112.phi nr.112.pin nr.112.pni nr.112.ppd nr.112.psd nr.112.psq nr.pal taxdb.bti

However, referencing the directory that contains all of these files as the database for the blast search does not seem to work and spits out the error above.

Is there any way to fix this? Or, is there any other way of making the nr database so that I can reference it as a single root file?

Thanks

BLAST command line • 1.4k views
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Entering edit mode
3.3 years ago
GenoMax 119k

What version of blast+ application are you using?

Note: You need to download the entire set of nr* files (all 112 of them). These are pre-formatted index files, so you don't need to do anything else (to make them usable) except un-compress.

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With new default blast+ v5 database, size of the files changed (individual files are now larger). There are only 38 files as of August 2020.