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  • Use of cutomized blastn datagase

    I have installed ncbi-blast-2.3.0 in my PC
    I have created a custom database (I think it is made of the 6 new files named after my database name with different extensions: .nhr .nin .nog .nds .nsi nsq)
    To interrogate this database with the sequence file abc.fsa, while within the directory containing the 6 files above I input:
    blastn -db custom_database_name -query abc.fsa
    I get the following message: Too many positional arguments (1), the offending value: -db
    What did I make wrong?
    Thanks in advance.

    Enrico

  • #2
    Are you using just the "basename" of the blast index as an argument for -db? Your query and database are both nucleotide sequences?

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    • #3
      Did you copy and paste the command, or type it directly? It should be a minus sign then db, but if you copied it from a PDF you can get a long dash symbol which looks like a minus sign but isn't. That would explain the error message.

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      • #4
        Good catch Peter. Smart hyphens (and related "smart" things) can cause unintended consequences on copy/paste. This is the most likely explanation here.

        Comment


        • #5
          Originally posted by GenoMax View Post
          Are you using just the "basename" of the blast index as an argument for -db? Your query and database are both nucleotide sequences?
          Thanks for your reply,
          yes the name of my database is MYCdb and I use such name as an argument of -db
          Both query and database are nucleotide sequences

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          • #6
            Did you look into @Peter's (maubp) suggestion or does that not apply?

            Comment


            • #7
              I tried again just now paying attention to use the minus;.
              Now I have a different error message: Unknown argument: title
              Actually typing
              blastn -help
              I do not see -title in the help-list
              Thanks everibody
              Enrico

              Comment


              • #8
                It works now, I was using -title instead of -db.
                Thanks everybody, sorry for my foolishness.

                Enrico

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