text: user2497: I have been attempting to map reads to a reference genome using HISAT2 using the Pertea, et al 2016 Nature Protocols paper. I am able to successfully generate an index (using the hisat2-build command), but when it comes to the actual mapping, I run into problems. The code I'm using (from the paper):
  $hisat2 -p 8 --dta -x daphnia_tran -1 C2*R1*.fastq -2 C2*R2*.fastq -S C2paired.sam
  
  And I get the error message:
  ./HISAT2_Basic_14.sh: line 26: -p: command not found
  
  When I remove the -p argument, the error message is similar, but says "--dta: command not found"
  Any ideas on what the issue is?
  Thank you!
  
  user77: tldr: Remove the $ from the command.
  I imagine you're literally typing $hisat2, where you mean to instead type hisat2. The $ is just meant to show the end of the command prompt. If you actually type $hisat2, you're not executing the hisat2 program, but whatever the $hisat2 variable is set to. Since it's likely not set to anything, it's just ignored. For example:
  ryan@maximus:~$ $hisat2 ls
  bin              convertChromosomesChain.py  ...
  
  Since there's no $hisat2 variable, I'm actually just running ls. Likewise, your command is just reducing to -p 8 --dta -x daphnia_tran -1 C2*R1*.fastq -2 C2*R2*.fastq -S C2paired.sam, which is the source of the error.
  
original_text: 2497: <p>I have been attempting to map reads to a reference genome using HISAT2 using the Pertea, et al 2016 Nature Protocols paper. I am able to successfully generate an index (using the hisat2-build command), but when it comes to the actual mapping, I run into problems. The code I'm using (from the paper):</p>
  
  <pre><code>$hisat2 -p 8 --dta -x daphnia_tran -1 C2*R1*.fastq -2 C2*R2*.fastq -S C2paired.sam
  </code></pre>
  
  <p>And I get the error message:</p>
  
  <pre><code>./HISAT2_Basic_14.sh: line 26: -p: command not found
  </code></pre>
  
  <p>When I remove the -p argument, the error message is similar, but says "--dta: command not found"</p>
  
  <p>Any ideas on what the issue is?</p>
  
  <p>Thank you!</p>
   77: <p>tldr: Remove the <code>$</code> from the command.</p>
  
  <p>I imagine you're literally typing <code>$hisat2</code>, where you mean to instead type <code>hisat2</code>. The <code>$</code> is just meant to show the end of the command prompt. If you actually type <code>$hisat2</code>, you're not executing the hisat2 program, but whatever the <code>$hisat2</code> variable is set to. Since it's likely not set to anything, it's just ignored. For example:</p>
  
  <pre><code>ryan@maximus:~$ $hisat2 ls
  bin              convertChromosomesChain.py  ...
  </code></pre>
  
  <p>Since there's no <code>$hisat2</code> variable, I'm actually just running <code>ls</code>. Likewise, your command is just reducing to <code>-p 8 --dta -x daphnia_tran -1 C2*R1*.fastq -2 C2*R2*.fastq -S C2paired.sam</code>, which is the source of the error.</p>
  