1
$\begingroup$

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

Improve this question
$\endgroup$
4
  • 1
    $\begingroup$ What is the output to which -a makeblastdb? $\endgroup$
    – Ram RS
    Dec 12, 2020 at 18:32
  • $\begingroup$ How did you install prokka? $\endgroup$
    – Maximilian Press
    Dec 12, 2020 at 21:41
  • $\begingroup$ It is installed by the admin. I work through the university server. $\endgroup$
    – ahmedbar
    Dec 13, 2020 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. $\endgroup$
    – Maximilian Press
    Dec 13, 2020 at 19:00

0

Reset to default

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.