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Old 05-21-2019, 01:33 PM   #1
sannazza
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Location: Argentina

Join Date: May 2019
Posts: 2
Default blast+ nt database

Hi all, I hope someone can help me!
I've downloaded and installed ncbi-blast-2.9.0+, then downloaded and decompressed the 71 files from the nt_v5 database. I followed NCBI instructions and created the paths to both the blast program and database.
However, when I try to run:

$ blastdbcmd -db database5 -info

I get the following:

BLAST Database error: No alias or index file found for nucleotide database [database5] in search path [/Users/Analia:/Users/Analia/miniconda3/bin:/Users/Analia/miniconda3/bin:/Users/Analia/miniconda3/bin:/Users/Analia/miniconda3/bin:/Users/Analia/miniconda3/bin:/Users/Analia/miniconda3/bin:/Users/Analia/miniconda3/bin:/Users/Analia/miniconda3/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/ncbi/blast/bin:/Users/Analia/ncbi-blast-2.9.0+:/Users/Analia/ncbi-blast-2.9.0+:/Users/Analia/ncbi-blast-2.9.0+/bin:/Users/Analia/ncbi-blast-2.9.0+/bin:/Users/Analia/miniconda3/bin:/Users/Analia/miniconda3/bin:/Users/Analia/miniconda3/bin:/Users/Analia/miniconda3/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/ncbi/blast/bin:/Users/Analia/ncbi-blast-2.9.0+:/Users/Analia/ncbi-blast-2.9.0+:/Users/Analia/ncbi-blast-2.9.0+/bin:/Users/Analia/ncbi-blast-2.9.0+/bin:/Users/Analia/ncbi-blast-2.9.0+/bin:/Users/Analia/ncbi-blast-2.9.0+/bin:/Users/Analia/ncbi-blast-2.9.0+/bin:/Users/Analia/database5:]

Can anyone tell me what am I doing wrong, please?
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Old 05-22-2019, 03:26 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,937
Default

You will need to use the name of the database you are looking to get information on.
Code:
$ blastdbcmd -db /path_to/blastv5/nt_v5 -info
Database: Nucleotide collection (nt)
        51,045,413 sequences; 202,915,260,500 total bases

Date: Mar 15, 2019  2:20 AM     Longest sequence: 99,791,824 bases

BLASTDB Version: 5

Volumes:
        /path_to/blastv5/nt_v5.00
        /path_to/blastv5/nt_v5.01
        /path_to/blastv5/nt_v5.02
..........
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Old 05-22-2019, 09:44 AM   #3
sannazza
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Location: Argentina

Join Date: May 2019
Posts: 2
Default

Quote:
Originally Posted by GenoMax View Post
You will need to use the name of the database you are looking to get information on.
Code:
$ blastdbcmd -db /path_to/blastv5/nt_v5 -info
Database: Nucleotide collection (nt)
        51,045,413 sequences; 202,915,260,500 total bases

Date: Mar 15, 2019  2:20 AM     Longest sequence: 99,791,824 bases

BLASTDB Version: 5

Volumes:
        /path_to/blastv5/nt_v5.00
        /path_to/blastv5/nt_v5.01
        /path_to/blastv5/nt_v5.02
..........
Thanks, it worked! From what I could understand by reading the blast+ manual, I didn't think it was necessary to use the database name nt_v5. I should have asked here before, thank you so much, GenoMax!
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