<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>

CC BY-SA 4.0
2023-01-11T16:49:19.237Z
Of course! It's now obvious `-b` or `--bed` would work. However `-bed` will not work @ИльяБетяев. Upvoted.
M__
CC BY-SA 4.0
2023-01-11T15:48:59.120Z
2023-01-11T15:48:59.120Z
terdon
<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>

<bed>
Problem with ClinCNV script
# 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, 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 @ИльяБетяев. Upvoted.  

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