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  • 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?

  • #2
    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
    ..........

    Comment


    • #3
      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!

      Comment

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