<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>

CC BY-SA 4.0
2020-12-12T18:32:51.950Z
What is the output to `which -a makeblastdb`?
Ram RS
CC BY-SA 4.0
2020-12-12T21:41:34.323Z
How did you install prokka?
Maximilian Press
CC BY-SA 4.0
2020-12-13T10:39:30.803Z
It is installed by the admin. I work through the university server.
ahmedbar
CC BY-SA 4.0
2020-12-13T19:00:19.347Z
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.
Maximilian Press
<phylogenetics><sequence-annotation><software-usage><orf>
Prokka error message
# 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- $OUTPUTFILE.gff /cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/prokka_A_C/$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 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.  

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## 0 answers

