text: user16725: I have some problems with ClinCNV:
  My input: Rscript /root/ClinCNV/clinCNV.R --normal /root/samples/final.cov --out /root/samples/ -bed /root/samples/fileGC.bed --folderWithScript /root/ClinCNV/
  And there is an output: /root/ClinCNV/clinCNV.R: error: Error in getopt(spec = spec, opt = args) : short flag "b" is invalid
  I've already ask a question about ClinCNV and the main idea was to run script with absolute pathways.
  
  user298: You are using -bed. Multi-letter flags are usually set using -- and not -. I don't know this particular program but since all other long options use --, and the only option with a b is your -bed, I suspect you just want --bed instead:
  Rscript /root/ClinCNV/clinCNV.R --normal /root/samples/final.cov \
     --out /root/samples/ \
     --bed /root/samples/fileGC.bed \
     --folderWithScript /root/ClinCNV/
  
  
  This is confirmed by the tool's documentation, actually:
  
  --bed - .bed file with coordinates of on-target regions, GC-annotated. Gene anotations in the last column can be used in output.
  
  So yes, you need --bed and not -bed. Because you used -, the tool reads that as a single character flag (-b) with the value ed and doesn't know what to do with it.
  
  On an unrelated note, you seem to be running these things as root which is a very, very bad idea. One bug in the program or one misconfiguration and you can mess up your entire system. I strongly urge you to never run commands as root unless absolutely necessary.
  
original_text: 16725: <p>I have some problems with ClinCNV:</p>
  <p>My input: <code>Rscript /root/ClinCNV/clinCNV.R --normal /root/samples/final.cov --out /root/samples/ -bed /root/samples/fileGC.bed --folderWithScript /root/ClinCNV/</code></p>
  <p>And there is an output: <code>/root/ClinCNV/clinCNV.R: error: Error in getopt(spec = spec, opt = args) : short flag &quot;b&quot; is invalid</code></p>
  <p>I've already ask a question about ClinCNV and the main idea was to run script with absolute pathways.</p>
   298: <p>You are using <code>-bed</code>. Multi-letter flags are usually set using <code>--</code> and not <code>-</code>. I don't know this particular program but since all other long options use <code>--</code>, and the only option with a <code>b</code> is your <code>-bed</code>, I suspect you just want <code>--bed</code> instead:</p>
  <pre><code>Rscript /root/ClinCNV/clinCNV.R --normal /root/samples/final.cov \
     --out /root/samples/ \
     --bed /root/samples/fileGC.bed \
     --folderWithScript /root/ClinCNV/
  </code></pre>
  <hr />
  <p>This is confirmed by the tool's <a href="https://github.com/imgag/ClinCNV" rel="nofollow noreferrer">documentation</a>, actually:</p>
  <blockquote>
  <p>--bed - .bed file with coordinates of on-target regions, GC-annotated. Gene anotations in the last column can be used in output.</p>
  </blockquote>
  <p>So yes, you need <code>--bed</code> and not <code>-bed</code>. Because you used <code>-</code>, the tool reads that as a single character flag (<code>-b</code>) with the value <code>ed</code> and doesn't know what to do with it.</p>
  <hr />
  <p>On an unrelated note, you seem to be running these things as root which is a very, very bad idea. One bug in the program or one misconfiguration and you can mess up your entire system. I strongly urge you to never run commands as root unless absolutely necessary.</p>
  