Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

      Latest Articles

      Collapse

      • seqadmin
        Strategies for Sequencing Challenging Samples
        by seqadmin


        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
        03-22-2024, 06:39 AM
      • seqadmin
        Techniques and Challenges in Conservation Genomics
        by seqadmin



        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

        Avian Conservation
        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
        03-08-2024, 10:41 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 06:37 PM
      0 responses
      8 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      8 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      49 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      67 views
      0 likes
      Last Post seqadmin  
      Working...
      X