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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

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    $\begingroup$ What is the output to which -a makeblastdb? $\endgroup$
    – Ram RS
    Dec 12 '20 at 18:32
  • $\begingroup$ How did you install prokka? $\endgroup$ Dec 12 '20 at 21:41
  • $\begingroup$ It is installed by the admin. I work through the university server. $\endgroup$
    – ahmedbar
    Dec 13 '20 at 10:39
  • $\begingroup$ 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. $\endgroup$ Dec 13 '20 at 19:00

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