<p>If you're in the RepeatScout directory you need to execute the Perl script with a <code>./</code> prefix, like so.</p>

<pre><code>cat od_1000_repeats.fa | ./filter-stage-1.prl &gt; od_1000_repeats_filt1.fa
</code></pre>

<p>If you're not in the RepeatScout directory, you need to provide the full relative or absolute path when executing the script. Alternatively, you can put the RepeatScout directory in your <code>$PATH</code> environmental variable.</p>

<p>These are all standard UNIX/Linux concepts that many bioinformaticians take for granted, for better and for worse. If you're lost in all the terminology, a crash course in UNIX basics is probably where you would want to start.</p>

CC BY-SA 4.0
2019-05-01T17:18:29.910Z
I installed repeatscout on my PC, I created the Repeatscout directory and It worked without errors. The problem is that it can't execute a file larger more than 800 mb in a 16 gb ram of my pc. So I had to use the cluster but I don't know where is the Repeatscout directory.(If I put "locate Repeatscout" I don't find it). I would to find the path to check if all the programs are correctly installed..
jonny
CC BY-SA 4.0
2019-05-01T18:12:21.600Z
It sounds like you need to get some help from your system administrator.
Daniel Standage
CC BY-SA 4.0
2019-05-01T15:50:29.220Z
2019-05-01T15:50:29.220Z
Daniel Standage
<p>I've installed Repeatscout from <a href="https://bix.ucsd.edu/repeatscout/" rel="nofollow noreferrer">https://bix.ucsd.edu/repeatscout/</a>.
I've also installed TRF and nseg required by the program. 
I followed the steps:</p>

<pre><code>build_lmer_table -l 16 -sequence ~/file_fasta/od_1000.fa -freq od_1000.freq
</code></pre>

<pre><code> RepeatScout -sequence od_1000.fa -output od_1000_repeats.fa -freq od_1000.freq -l 16
</code></pre>

<p>and the I put this command:</p>

<pre><code>cat od_1000_repeats.fa| filter-stage-1.prl &gt;od_1000_repeats_filt1.fa 
</code></pre>

<p>but this message appears:</p>

<pre><code>bash: filter-stage-1.prl: command not found...
</code></pre>

<p>Why? It is all correctly installed, I can't understand the problem</p>

<software-installation>
Repeatscout installation problem
# Repeatscout installation problem

(Asked by: username_0 on 2019-05-01)

I've installed Repeatscout from https://bix.ucsd.edu/repeatscout/.
I've also installed TRF and nseg required by the program. 
I followed the steps:
build_lmer_table -l 16 -sequence ~/file_fasta/od_1000.fa -freq od_1000.freq

 RepeatScout -sequence od_1000.fa -output od_1000_repeats.fa -freq od_1000.freq -l 16

and the I put this command:
cat od_1000_repeats.fa| filter-stage-1.prl >od_1000_repeats_filt1.fa 

but this message appears:
bash: filter-stage-1.prl: command not found...

Why? It is all correctly installed, I can't understand the problem

**Tags:** software-installation

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## 1 answers

### Answer by username_1 on 2019-05-01. Score: 2 | Accepted answer

If you're in the RepeatScout directory you need to execute the Perl script with a ./ prefix, like so.
cat od_1000_repeats.fa | ./filter-stage-1.prl > od_1000_repeats_filt1.fa

If you're not in the RepeatScout directory, you need to provide the full relative or absolute path when executing the script. Alternatively, you can put the RepeatScout directory in your $PATH environmental variable.
These are all standard UNIX/Linux concepts that many bioinformaticians take for granted, for better and for worse. If you're lost in all the terminology, a crash course in UNIX basics is probably where you would want to start.

> **Comments:**
> **username_0**: I installed repeatscout on my PC, I created the Repeatscout directory and It worked without errors. The problem is that it can't execute a file larger more than 800 mb in a 16 gb ram of my pc. So I had to use the cluster but I don't know where is the Repeatscout directory.(If I put "locate Repeatscout" I don't find it). I would to find the path to check if all the programs are correctly installed..  
> **username_1**: It sounds like you need to get some help from your system administrator.  

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