Answers.Body: <p>My suggestion is to run <code>prokka</code> from within <code>conda</code> by simply downloading <a href="https://docs.conda.io/projects/conda/en/stable/user-guide/install/download.html" rel="nofollow noreferrer">miniconda</a> then</p>
  <pre><code>conda create --name prokka
  conda activate prokka
  conda install -c conda-forge -c bioconda -c defaults prokka
  prokka --help
  prokka --version
  prokka mycontigs.fa # running prokka
  </code></pre>
  <p>You could always perform a</p>
  <pre><code>chmod 700 /home/saurab/BIOIN/phastest-app/sub_programs/barrnap
  </code></pre>
  <p>or some variant like <code>chmod 500 ...</code></p>
  <p>or possibly using a recursive <code>chmod -R 500</code> that sort of thing. Eventually it will work.</p>
  <p><strong>However</strong>, it strikes me you are installing <code>prokka</code> outside any virtual environment such as <code>conda</code> or <code>brew</code> and I would not do that personally, because you are giving significant permissions to the algorithm.</p>
  <p><code>conda</code> (or <code>brew</code>) will sort out all the permission needed and there's no need to do anything with <code>chmod</code> stuff.</p>
  <p>Good luck with the annotation.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-02-23T22:57:28.020Z
Answers.LastActivityDate: 2023-02-24T18:42:06.677Z
Answers.LastEditDate: 2023-02-24T18:42:06.677Z
Answers.UserDisplayName: M__
Body: <p>I am trying to run the <strong>Prokka annotation tool</strong> on my linux machine and have installed <strong>Barrnap and added it to $PATH and given the folder chmod 777 permission</strong>. However, when running Prokka, it gives the line <code>Could not parse version from 'sh: 1: barrnap: Permission denied'</code>.</p>
  <p>Running Barrnap solely through the command line with a valid input works fine but does not seem to work when another script calls barrnap. I have tried checking path variables and giving max permissions to barrnap and Prokka but it does not seem to change this error. Here is the full log file:</p>
  <pre><code>[15:01:28] This is prokka 1.14.6
  [15:01:28] Written by Torsten Seemann &lt;torsten.seemann@gmail.com&gt;
  [15:01:28] Homepage is https://github.com/tseemann/prokka
  [15:01:28] Local time is Thu Feb 23 15:01:28 2023
  [15:01:28] You are saurab
  [15:01:28] Operating system is linux
  [15:01:28] You have BioPerl 1.7.8
  [15:01:28] System has 16 cores.
  [15:01:28] Will use maximum of 8 cores.
  [15:01:28] Annotating as &gt;&gt;&gt; Bacteria &lt;&lt;&lt;
  [15:01:28] Generating locus_tag from 'jobs/NC_004556.faa' contents.
  [15:01:28] Setting --locustag ECJHPMJE from MD5 ec31963ed5d3d76e28501fa7e45ca273
  [15:01:28] Creating new output folder: PROKKA_02232023
  [15:01:28] Running: mkdir -p PROKKA_02232023
  [15:01:28] Using filename prefix: PROKKA_02232023.XXX
  [15:01:28] Setting HMMER_NCPU=1
  [15:01:28] Writing log to: PROKKA_02232023/PROKKA_02232023.log
  [15:01:28] Command: /home/saurab/BIOIN/basys2-app/sub_programs/prokka/bin/prokka jobs/NC_004556.faa
  [15:01:28] Appending to PATH: /home/saurab/BIOIN/basys2-app/sub_programs/prokka/bin/../binaries/linux
  [15:01:28] Appending to PATH: /home/saurab/BIOIN/basys2-app/sub_programs/prokka/bin/../binaries/linux/../common
  [15:01:28] Appending to PATH: /home/saurab/BIOIN/basys2-app/sub_programs/prokka/bin
  [15:01:28] Looking for 'aragorn' - found /home/saurab/BIOIN/phastest-app/sub_programs/aragorn
  [15:01:28] Determined aragorn version is 001002 from 'ARAGORN v1.2   Dean Laslett'
  [15:01:28] Looking for 'barrnap' - found /home/saurab/BIOIN/phastest-app/sub_programs/barrnap
  [15:01:28] Coult not parse version from 'sh: 1: barrnap: Permission denied'
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-02-24T09:28:44.823Z
Comments.Text: Please [edit] your question and add the output of `ls -l /home/saurab/BIOIN/phastest-app/sub_programs/barrnap`. You say you set the directory to 777 but what about the actual script/executable?
Comments.UserDisplayName: terdon
Tags: <sequence-annotation><perl><bacteria><functional-annotation>
Title: Barrnap Bacterial rRNA Predictor script permission denied error when running Prokka
ThreadText: # Barrnap Bacterial rRNA Predictor script permission denied error when running Prokka
  
  (Asked by: username_0 on 2023-02-23)
  
  I am trying to run the **Prokka annotation tool** on my linux machine and have installed **Barrnap and added it to $PATH and given the folder chmod 777 permission**. However, when running Prokka, it gives the line `Could not parse version from 'sh: 1: barrnap: Permission denied'`.
  
  Running Barrnap solely through the command line with a valid input works fine but does not seem to work when another script calls barrnap. I have tried checking path variables and giving max permissions to barrnap and Prokka but it does not seem to change this error. Here is the full log file:
  
  ```
  [15:01:28] This is prokka 1.14.6
  [15:01:28] Written by Torsten Seemann <torsten.seemann@gmail.com>
  [15:01:28] Homepage is https://github.com/tseemann/prokka
  [15:01:28] Local time is Thu Feb 23 15:01:28 2023
  [15:01:28] You are saurab
  [15:01:28] Operating system is linux
  [15:01:28] You have BioPerl 1.7.8
  [15:01:28] System has 16 cores.
  [15:01:28] Will use maximum of 8 cores.
  [15:01:28] Annotating as >>> Bacteria <<<
  [15:01:28] Generating locus_tag from 'jobs/NC_004556.faa' contents.
  [15:01:28] Setting --locustag ECJHPMJE from MD5 ec31963ed5d3d76e28501fa7e45ca273
  [15:01:28] Creating new output folder: PROKKA_02232023
  [15:01:28] Running: mkdir -p PROKKA_02232023
  [15:01:28] Using filename prefix: PROKKA_02232023.XXX
  [15:01:28] Setting HMMER_NCPU=1
  [15:01:28] Writing log to: PROKKA_02232023/PROKKA_02232023.log
  [15:01:28] Command: /home/saurab/BIOIN/basys2-app/sub_programs/prokka/bin/prokka jobs/NC_004556.faa
  [15:01:28] Appending to PATH: /home/saurab/BIOIN/basys2-app/sub_programs/prokka/bin/../binaries/linux
  [15:01:28] Appending to PATH: /home/saurab/BIOIN/basys2-app/sub_programs/prokka/bin/../binaries/linux/../common
  [15:01:28] Appending to PATH: /home/saurab/BIOIN/basys2-app/sub_programs/prokka/bin
  [15:01:28] Looking for 'aragorn' - found /home/saurab/BIOIN/phastest-app/sub_programs/aragorn
  [15:01:28] Determined aragorn version is 001002 from 'ARAGORN v1.2   Dean Laslett'
  [15:01:28] Looking for 'barrnap' - found /home/saurab/BIOIN/phastest-app/sub_programs/barrnap
  [15:01:28] Coult not parse version from 'sh: 1: barrnap: Permission denied'
  
  ```
  
  **Tags:** sequence-annotation, perl, bacteria, functional-annotation
  
  > **Comments:**
  > **username_1**: Please [edit] your question and add the output of `ls -l /home/saurab/BIOIN/phastest-app/sub_programs/barrnap`. You say you set the directory to 777 but what about the actual script/executable?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2023-02-23. Score: 3 | Accepted answer
  
  My suggestion is to run `prokka` from within `conda` by simply downloading [miniconda](https://docs.conda.io/projects/conda/en/stable/user-guide/install/download.html) then
  
  ```
  conda create --name prokka
  conda activate prokka
  conda install -c conda-forge -c bioconda -c defaults prokka
  prokka --help
  prokka --version
  prokka mycontigs.fa # running prokka
  
  ```
  
  You could always perform a
  
  ```
  chmod 700 /home/saurab/BIOIN/phastest-app/sub_programs/barrnap
  
  ```
  
  or some variant like `chmod 500 ...`
  
  or possibly using a recursive `chmod -R 500` that sort of thing. Eventually it will work.
  
  **However**, it strikes me you are installing `prokka` outside any virtual environment such as `conda` or `brew` and I would not do that personally, because you are giving significant permissions to the algorithm.
  
  `conda` (or `brew`) will sort out all the permission needed and there's no need to do anything with `chmod` stuff.
  
  Good luck with the annotation.
  
  
  ---
  
  