text: user7236: I have DNA sample from 5 pools, having 25 fastq files each. I am running cutadapt to remove the primers using this command 
  cutadapt -g ACTTAAGTGTATGTAAACTTCCGACTTCAACTG A7_S7_R1_001.fastq -o sb_A7_S7_R1_001.fastq --discard-untrimmed
  However, this is too time consuming.  I tried my hand at writing shell script
  for file in /dir/*
  do
    cmd cutadapt -g ACTTAAGTGTATGTAAACTTCCGACTTCAACTG "$file" >> results.out
  done
  
  But it is not running . 
  Can someone help.
  Thanks
  
  user175: Try this one
  for file in /dir/*
  do
    cutadapt -g ACTTAAGTGTATGTAAACTTCCGACTTCAACTG "$file" >> results.out
  done
  
  Also you have omitted --discard-untrimmed from the original command. If you want that as well along with everything to run in parallel:
  for file in /dir/*
  do
    cutadapt -g ACTTAAGTGTATGTAAACTTCCGACTTCAACTG --discard-untrimmed "$file" -o "`basename -s .fastq $file`_out.fastq" &
  done
  
  
original_text: 7236: <p>I have DNA sample from 5 pools, having 25 fastq files each. I am running cutadapt to remove the primers using this command 
  <code>cutadapt -g ACTTAAGTGTATGTAAACTTCCGACTTCAACTG A7_S7_R1_001.fastq -o sb_A7_S7_R1_001.fastq --discard-untrimmed</code>
  However, this is too time consuming.  I tried my hand at writing shell script</p>
  
  <pre><code>for file in /dir/*
  do
    cmd cutadapt -g ACTTAAGTGTATGTAAACTTCCGACTTCAACTG "$file" &gt;&gt; results.out
  done
  </code></pre>
  
  <p>But it is not running . 
  Can someone help.
  Thanks</p>
   175: <p>Try this one</p>
  
  <pre><code>for file in /dir/*
  do
    cutadapt -g ACTTAAGTGTATGTAAACTTCCGACTTCAACTG "$file" &gt;&gt; results.out
  done
  </code></pre>
  
  <p>Also you have omitted <code>--discard-untrimmed</code> from the original command. If you want that as well along with everything to run in parallel:</p>
  
  <pre><code>for file in /dir/*
  do
    cutadapt -g ACTTAAGTGTATGTAAACTTCCGACTTCAACTG --discard-untrimmed "<span class="math-container">$file" -o "`basename -s .fastq $</span>file`_out.fastq" &amp;
  done
  </code></pre>
  