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  • Blastn error: positional arguments ?

    Hi, a beginner here!

    I am trying to run a blast search using a local datbase.

    I create the local db using a multifasta file:
    makeblastdb -in /root/reference/multiseq.fasta -dbtype 'nucl' -out /root/reference/dbname
    this create 3 files in root/reference/dbname: dbname.nhr, .nin and .nsq

    then I run:
    blastn –db /root/reference/db/dbname –query /root/data/seq.fa –out /root/data/seq_blast_results.out

    but I got this error message:Error: Too many positional arguments (1), the offending value: –db

    Is the local db is correctly created? could you help?

    Thanks

  • #2
    Originally posted by bpich View Post
    ...this create 3 files in root/reference/dbname: dbname.nhr, .nin and .nsq

    then I run:
    blastn –db /root/reference/db/dbname –query /root/data/seq.fa –out /root/data/seq_blast_results.out
    root/reference/dbname vs. /root/reference/db/dbname

    May that be your problem?

    What happens if you just type:
    Code:
    -db dbname

    Comment


    • #3
      my mistake! the cmd is
      blastn –db /root/reference/dbname –query /root/data/seq.fa –out /root/data/seq_blast_results.out

      Comment


      • #4
        Try the solution recommended by A. Mstt in this thread: http://stackoverflow.com/questions/2...ending-value-f

        Comment


        • #5
          Many thanks. work perfectly now

          Comment

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