Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-06T14:09:15.357Z
Answers.Text: Thanks for the comment - I've tried multiple ways to get rid of this, including typing out from hand, copying/pasting, and even copying the '-' that shows up when i type ```blastn -help```, however I'm still getting the same error. Just to be clear, dashes ('-') refer to the 'minus' sign next to 0 right? (I'm a Mac user)
Answers.UserDisplayName: aislinx
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-06T14:26:17.553Z
Answers.Text: The only think that I can think of is the `$db` variable. Does it somehow contain whitespaces or any other character that the shell would not understand? If the tilde sign (`~`) is part of what `$db` corresponds to (like in your question), you can try changing it to the exact path of your database.
Answers.UserDisplayName: haci
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Answers.CreationDate: 2020-03-06T14:34:09.893Z
Answers.Text: I've just tried ```blastn -db ~/5030/hw2/db -query seqs.fas -out q1results.txt
  ```
  but that just straight up shows me a ```BLAST Database rror: no alias or index file found for nucleotide database in search path```
Answers.UserDisplayName: aislinx
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-06T15:34:06.347Z
Answers.Text: This is another error, I guess you point out to the wrong database path.
Answers.UserDisplayName: haci
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-06T15:35:21.450Z
Answers.Text: Just to be clear, when i'm doing -db, to which should I refer to: the directory where I have my database, or the entire DB path?
Answers.UserDisplayName: aislinx
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Answers.UserDisplayName: haci
Body: <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>
  
Tags: <blastn>
Title: using blastn to search [error]
ThreadText: # using blastn to search [error]
  
  (Asked by: username_0 on 2020-03-06)
  
  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!
  
  **Tags:** blastn
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-03-06. Score: 2
  
  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](http://www.metagenomics.wiki/tools/blast/error-too-many-positional-arguments).
  
  > Problem is a copy & past from the BLAST documentation, all dashes
  > ('–') need to be replaced by hand at the command line.
  
  > **Comments:**
  > **username_0**: Thanks for the comment - I've tried multiple ways to get rid of this, including typing out from hand, copying/pasting, and even copying the '-' that shows up when i type ```blastn -help```, however I'm still getting the same error. Just to be clear, dashes ('-') refer to the 'minus' sign next to 0 right? (I'm a Mac user)  
  > **username_1**: The only think that I can think of is the `$db` variable. Does it somehow contain whitespaces or any other character that the shell would not understand? If the tilde sign (`~`) is part of what `$db` corresponds to (like in your question), you can try changing it to the exact path of your database.  
  > **username_0**: I've just tried ```blastn -db ~/5030/hw2/db -query seqs.fas -out q1results.txt ``` but that just straight up shows me a ```BLAST Database rror: no alias or index file found for nucleotide database in search path```  
  > **username_1**: This is another error, I guess you point out to the wrong database path.  
  > **username_0**: Just to be clear, when i'm doing -db, to which should I refer to: the directory where I have my database, or the entire DB path?  
  
  ---
  
  