Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-01-11T16:49:19.237Z
Answers.Text: Of course! It's now obvious `-b` or `--bed` would work. However `-bed` will not work @ИльяБетяев. Upvoted.
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Body: <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>
  
Tags: <bed>
Title: Problem with ClinCNV script
ThreadText: # Problem with ClinCNV script
  
  (Asked by: username_0 on 2023-01-11)
  
  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.
  
  **Tags:** bed
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2023-01-11. Score: 3 | Accepted answer
  
  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](https://github.com/imgag/ClinCNV), 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.
  
  > **Comments:**
  > **username_2**: Of course! It's now obvious `-b` or `--bed` would work. However `-bed` will not work @username_0. Upvoted.  
  
  ---
  
  