Command line blast database problem

Question

[jolespin]

So I downloaded the ncbi blast suite and I'm trying to run the command line.

I have a text file with a protein sequence at ~/in.txt:

MWLGLCLSLPPEFPGLDFTALCPLLQEAQPVWPCDLQVLESHS*

I used scp to copy the database files from my school [UCSC] server to my local drive in ~/blast_db

I ran the following command:

blastp -query ~/in.txt -out output_blast.txt -db /Users/Mu/blast_db/nr.32.psq

This is my error:

eduroam-16180339887:~ Mu$ blastp -db ~/blast_db/nr.32.psq -query ~/in.txt -out output_blast.txt
BLAST Database error: No alias or index file found for protein database [/Users/Mu/blast_db/nr.32.psq] in search path [/Users/Mu::]

The files are binary for the database. I looked up the suffix on NCBI and .psq is what to use for protein database. How can I get this to work?

Answer 1

[h.mon]

I think your command-line should be:

blastp -query ~/in.txt -out output_blast.txt -db /Users/Mu/blast_db/nr.32

Do you have the other nr.32 files in addition to the .psq?

[jolespin]

Yes I do. Woah it worked. Why didn't it work with ~/blast_db/nr.32.psq? ~ = /Users/Mu/

[h.mon]

Because blast was looking for files nr.32.psq.psq, nr.32.psq.pni, etc.