BLAST: can't find reference file in db

Question

[kelvinfrog75]

I am trying to run the standalone ncbi-blast-2.2.29+ on my machine (Mac) but get this error message when running blastx (or blastn) with my database:

No alias or index file found for nucleotide database [db/viral.1.1.genomic] in search path [~/Users/KK/ncbi-blast-2.3.0+/Virus::]

The way I run it:

blastn -query input.fasta -out out.blast.txt -db db/viral.1.1.genomic

My working directory is ~/Users/KK/ncbi-blast-2.3.0+/Virus and there is a sub-directory db (~/Users/KK/ncbi-blast-2.3.0+/Virus/db) and db has viral.1.1.genomic.phr, viral.1.1.genomic.pin, viral.1.1.genomic.pnd, viral.1.1.genomic.pni, viral.1.1.genomic.pog, viral.1.1.genomic.psd, viral.1.1.genomic.psi, viral.1.1.genomic.psq, viral.1.1.genomic.fasta. and I made all these files using this command line

makeblastdb -in viral.1.1.genomic.fasta -out viral1.1.genomic -dbtype prot -parse_seqids

I just don't know why I keep getting error message saying no alias or index file found. I have read other similar questions posted by others but don't seem finding answer to my problem. And I try other tblast and blastx and both of them return similar error except it said protein database instead of nucleotide

Answer 1

[Michael]

blastn is looking for a nucleotide database (with a .nin file) while you have created a protein database (with a .pin file):

...-out viral1.1.genomic -dbtype prot ...

You need to find out if your file viral.1.1.genomic.fasta contains AA or DNA sequence (most likely), then set the dbtype accordingly (nucl or prot). You can then use the db with blastn and tblastn and tblastx, but not with blatsp, and blastx. Check your db with

blastdbcmd -info

for details.

[kelvinfrog75]

It works. Thanks a lot