text: user7295: so I'm fairly new to using linux and blast - have encountered an error in my work. 
  I have created a fasta database with the results in this directory path: 
  ~/class/hw/db
  I'm currently trying to run a search against my created database against query sequences in a file called seqs.fas. 
  My code is as follows: 
  blastn -db $db -query seqs.fas -out q1results.txt
  However I keep getting this error: 
  Error: Too many positional arguments (1), the offending value: seqs.fas
  Error:  (CArgException::eSynopsis) Too many positional arguments (1), the offending value: seqs.fas
  I'm not sure what I'm doing wrong here, and would appreciate any advice to fix this, thanks!
  
  user3541: I remember having this problem in the past, it was encoding related. Rewriting the -s manually (the dash sign) should fix the issue, please see this.
  
  Problem is a copy & past from the BLAST documentation, all dashes
    ('–') need to be replaced by hand at the command line.
  
  
original_text: 7295: <p>so I'm fairly new to using linux and blast - have encountered an error in my work. </p>
  
  <p>I have created a fasta database with the results in this directory path: 
  <code>~/class/hw/db</code></p>
  
  <p>I'm currently trying to run a search against my created database against query sequences in a file called <code>seqs.fas</code>. </p>
  
  <p>My code is as follows: 
  <code>blastn -db $db -query seqs.fas -out q1results.txt</code></p>
  
  <p>However I keep getting this error: 
  <code>Error: Too many positional arguments (1), the offending value: seqs.fas</code></p>
  
  <p><code>Error:  (CArgException::eSynopsis) Too many positional arguments (1), the offending value: seqs.fas</code></p>
  
  <p>I'm not sure what I'm doing wrong here, and would appreciate any advice to fix this, thanks!</p>
   3541: <p>I remember having this problem in the past, it was encoding related. Rewriting the <code>-</code>s manually (the dash sign) should fix the issue, please see <a href="http://www.metagenomics.wiki/tools/blast/error-too-many-positional-arguments" rel="nofollow noreferrer">this</a>.</p>
  
  <blockquote>
    <p>Problem is a copy &amp; past from the BLAST documentation, all dashes
    ('–') need to be replaced by hand at the command line.</p>
  </blockquote>
  