Body: <p>I am trying to run Prokka but the following error message appears:</p>
  <blockquote>
  <p>Could not run command: makeblastdb -hash_index -dbtype prot -in /cluster/software/prokka/1.13.7-gompi-2019a/db/kingdom/Archaea/sprot -logfile /dev/null</p>
  </blockquote>
  <p>When I removed the <code>--setupdb</code>, the following error message appeared:</p>
  <blockquote>
  <p>The sequence databases have not been indexed. Please run 'prokka --setupdb' first</p>
  </blockquote>
  <p>after that, I changed my script to</p>
  <pre><code>prokka --setupdb --kingdom Bacteria -o <span class="math-container">$OUTPUTFILE.txt o- $</span>OUTPUTFILE.tsv o- <span class="math-container">$OUTPUTFILE.tbl o- $</span>OUTPUTFILE.faa o- <span class="math-container">$OUTPUTFILE.gff /cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/prokka_A_C/$</span>SAMPLE_ID_1
  </code></pre>
  <p>and still not working and the following error message appeared</p>
  <blockquote>
  <p>Could not run command: makeblastdb -hash_index -dbtype prot -in /cluster/software/prokka/1.13.4-foss-2018b/db/kingdom/Archaea/sprot -logfile /dev/null</p>
  </blockquote>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-12T18:32:51.950Z
Comments.Text: What is the output to `which -a makeblastdb`?
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-12T21:41:34.323Z
Comments.Text: How did you install prokka?
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-13T10:39:30.803Z
Comments.Text: It is installed by the admin. I work through the university server.
Comments.UserDisplayName: ahmedbar
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-13T19:00:19.347Z
Comments.Text: i think the answer to Ram RS's question will be crucial. what happens when you try to run `makeblastdb -hash_index -dbtype prot -in /cluster/software/prokka/1.13.4-foss-2018b/db/kingdom/Archaea/sprot` ? I wonder if you don't have write permissions to that directory, so it's failing. I would suggest contacting your admin, who will have a better idea of your setup than we have.
Comments.UserDisplayName: Maximilian Press
Tags: <phylogenetics><sequence-annotation><software-usage><orf>
Title: Prokka error message
ThreadText: # Prokka error message
  
  (Asked by: username_0 on 2020-12-12)
  
  I am trying to run Prokka but the following error message appears:
  
  > Could not run command: makeblastdb -hash\_index -dbtype prot -in /cluster/software/prokka/1.13.7-gompi-2019a/db/kingdom/Archaea/sprot -logfile /dev/null
  
  When I removed the `--setupdb`, the following error message appeared:
  
  > The sequence databases have not been indexed. Please run 'prokka --setupdb' first
  
  after that, I changed my script to
  
  ```
  prokka --setupdb --kingdom Bacteria -o $OUTPUTFILE.txt o- $OUTPUTFILE.tsv o- $OUTPUTFILE.tbl o- $OUTPUTFILE.faa o- $OUTPUTFILE.gff /cluster/work/users/username_0/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/prokka_A_C/$SAMPLE_ID_1
  
  ```
  
  and still not working and the following error message appeared
  
  > Could not run command: makeblastdb -hash\_index -dbtype prot -in /cluster/software/prokka/1.13.4-foss-2018b/db/kingdom/Archaea/sprot -logfile /dev/null
  
  **Tags:** phylogenetics, sequence-annotation, software-usage, orf
  
  > **Comments:**
  > **username_1**: What is the output to `which -a makeblastdb`?  
  > **username_2**: How did you install prokka?  
  > **username_0**: It is installed by the admin. I work through the university server.  
  > **username_2**: i think the answer to username_1's question will be crucial. what happens when you try to run `makeblastdb -hash_index -dbtype prot -in /cluster/software/prokka/1.13.4-foss-2018b/db/kingdom/Archaea/sprot` ? I wonder if you don't have write permissions to that directory, so it's failing. I would suggest contacting your admin, who will have a better idea of your setup than we have.  
  
  ---
  
  ## 0 answers
  
  