Seqanswers Leaderboard Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • silasysh
    Junior Member
    • Aug 2014
    • 5

    Blast2go pipeline

    dear all,

    I have two questions about blast2go.

    1. Is the blast2go pipeline(b2g4pipe) still free to use. Because I checked the website of Blast2Go. The command line version need to buy. Are there any free software likw Blast2Go and it is free?

    2. I still have the version 2.5 of b2g4pipe. Today, I tried to run it again. I found I can not connect to database b2g_aug12 anymore, the error message is the following:

    Problem connecting to database b2g_aug12 on publicdb.blast2go.com as blast2go with password starts with bla*****: Syntax error or access violation, message from server: "Access denied for user 'blast2go'@'%' to database 'b2g_aug12'"
    Database or network connection (timeout) error for: publicdb.blast2go.com
    Annotation of 0 seqs with 0 annots finished. Now searching for orfan IPRs...
    B2G-Pipe finished

    Could somebody gives me a suggestion?

    Thank you.

    Silas
  • maubp
    Peter (Biopython etc)
    • Jul 2009
    • 1544

    #2
    The good news is that b2g4pipe v2.5 is still freely available at http://www.blast2go.com/data/blast2go/b2g4pipe_v2.5.zip

    This was working fine for me with automated testing for my Galaxy Blast2GO (for pipelines) wrapper against the older b2g_jun11 database until a few weeks ago. In the short term I disabled the test, but have not had time to investigate if a more recent database is still available to this older version of Blast2GO: https://github.com/peterjc/galaxy_bl...982c1f9fef6987

    Note that I did see network/connection failures from time to time - so you should retest your system, perhaps at different times of day to try and connect at a low usage time (e.g. very early morning in Spain, late night in USA).

    However, it is clear that from v3 onwards BioBam Bioinformatics will be charging for the command line tool. It is possible they might stop supporting v2.x before too long, and given most people use their public database this would force upgrades. Wait and see?

    Comment

    • silasysh
      Junior Member
      • Aug 2014
      • 5

      #3
      Thank you for your reply. At least the package v2.5 is still free. I found the current database becomes b2g_sep13. Now everything is okay.

      Silas

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Pathogen Surveillance with Advanced Genomic Tools
        by seqadmin




        The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...
        03-24-2025, 11:48 AM
      • seqadmin
        New Genomics Tools and Methods Shared at AGBT 2025
        by seqadmin


        This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

        The Headliner
        The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
        03-03-2025, 01:39 PM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 03-20-2025, 05:03 AM
      0 responses
      49 views
      0 reactions
      Last Post seqadmin  
      Started by seqadmin, 03-19-2025, 07:27 AM
      0 responses
      57 views
      0 reactions
      Last Post seqadmin  
      Started by seqadmin, 03-18-2025, 12:50 PM
      0 responses
      50 views
      0 reactions
      Last Post seqadmin  
      Started by seqadmin, 03-03-2025, 01:15 PM
      0 responses
      201 views
      0 reactions
      Last Post seqadmin  
      Working...