text: user1075: I have successfully downloaded the whole nt BLAST database into the current folder using:
  wget -b "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.??.tar.gz" 
  
  However, I would like to download it in a specific folder, e.g. output/
  I have tried:
  wget -b "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.??.tar.gz"  -O output/
  
  but it does not work. Nothing happens. My 'wget-log' is empty.
  I could move to that folder and download it there but I would like to remain in the same working directory.
  C.
  
  user581: -O is to specify the name of the output file. You want the -P option.
  So, from your example
  wget -b "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.??.tar.gz" -P output/
  
  
original_text: 1075: <p>I have successfully downloaded the whole nt BLAST database into the current folder using:</p>
  
  <pre><code>wget -b "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.??.tar.gz" 
  </code></pre>
  
  <p>However, I would like to download it in a specific folder, e.g. output/</p>
  
  <p>I have tried:</p>
  
  <pre><code>wget -b "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.??.tar.gz"  -O output/
  </code></pre>
  
  <p>but it does not work. Nothing happens. My 'wget-log' is empty.</p>
  
  <p>I could move to that folder and download it there but I would like to remain in the same working directory.</p>
  
  <p>C.</p>
   581: <p><code>-O</code> is to specify the name of the output <em>file.</em> You want the <a href="https://stackoverflow.com/questions/1078524/how-to-specify-the-location-with-wget"><code>-P</code></a> option.</p>
  
  <p>So, from your example</p>
  
  <pre><code>wget -b "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.??.tar.gz" -P output/
  </code></pre>
  