Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Command line Blast.. not as good as it was?

    Hi All,

    I just have a general question for everyone who regularly uses command line blast with '-remote' i.e. using NCBI online databases. I'm using BLAST 2.6.0+ and I consistently get errors that are related to the NCBI server.. busy, overload, query too big, too many queries.. e.g. below. But the errors are random and its difficult to script repeating a failed blast when its seemingly random and can take a long time before it even errors.

    I think these problems have been getting worse and NCBI only tells me to use the browser version or submit fewer / smaller jobs (LOL).

    So just wondering what others' thoughts are? I think I'll have to give up and download a local copy of the dbs.

    Thanks,

    S.

    example:
    Error: (308.5) [blastn] [blast4] Service not found
    Error: (315.2) [blastn] CConn_Streambuf::CConn_Streambuf(): NULL connector: Unknown
    Error: (308.5) [blastn] [blast4] Service not found
    Error: (315.2) [blastn] CConn_Streambuf::CConn_Streambuf(): NULL connector: Unknown
    Error: (802.5) [blastn] CObjectOStream: error at byte 52: stack is empty: write fault
    Error: (802.5) [blastn] CObjectOStream: error at byte 0: stack is empty: cannot close output stream
    Error: (CIOException::eFlush) [blastn] COStreamBuffer::Flush: failed
    Error: (CSerialException::eIoError) [blastn] byte 0: cannot close output stream
    Error: (802.4) [blastn] Cannot close serializing output stream (CSerialException::eIoError) byte 0: cannot close output stream

    but lots of others too..
    0
    YES
    0%
    0
    NO
    0%
    0
    Last edited by susanklein; 02-20-2018, 04:57 PM. Reason: forgot example

  • #2
    The remote option is a convenience for those who don't have access to local hardware infrastructure to download copies of blast databases. If you have a need to run scores of jobs regularly then running blast locally should be your first choice. It is a free service after all.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      The Impact of AI in Genomic Medicine
      by seqadmin



      Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
      02-26-2024, 02:07 PM
    • seqadmin
      Multiomics Techniques Advancing Disease Research
      by seqadmin


      New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

      A major leap in the field has
      ...
      02-08-2024, 06:33 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 02-28-2024, 06:12 AM
    0 responses
    21 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-23-2024, 04:11 PM
    0 responses
    69 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-21-2024, 08:52 AM
    0 responses
    77 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-20-2024, 08:57 AM
    0 responses
    67 views
    0 likes
    Last Post seqadmin  
    Working...
    X