Question: Command line blast database problem
0
gravatar for jolespin
3.8 years ago by
jolespin120
United States
jolespin120 wrote:

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? 

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by jolespin120
2
gravatar for h.mon
3.8 years ago by
h.mon24k
Brazil
h.mon24k wrote:

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?

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by h.mon24k

yes i do. woah it worked.  why didn't it work with ~/blast_db/nr.32.psq ?  ~ = /Users/Mu/

ADD REPLYlink written 3.8 years ago by jolespin120

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

ADD REPLYlink written 3.8 years ago by h.mon24k
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