Prokka error message

Question

[a.mostafa5050]

Hi everybody, 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

Here is my SLURM script:

module load prokka/1.13.7-gompi-2019a
prokka --setupdb -i /cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/Contigs_and_scafolds_2/contigs_F-1year-Amox_S15.fasta -o /cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/CD_HIT_output

Thanks

[a.mostafa5050]

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

[Mensur Dlakic]

You need to run prokka --setupdb as a separate command, not like you are doing. Chances are that you can't do so without admin privileges because it probably requires writing in system directories, which is why you are getting the Could not run command: error. You may need to ask the system admin to set up databases first.

[a.mostafa5050]

But the database is found and I got this message before the error message Looking for 'makeblastdb' - found /cluster/software/prokka/1.13.4-foss-2018b/bin/../binaries/linux/makeblastdb

[Mensur Dlakic]

The database is found but it is not formatted. That's why you need to format it using prokka --setupdb. So the next thing is to do that using makeblastdb which is also found, but when it comes to using the program you get the error. Most likely this is because you don't have permissions to write in those directories where the database is located. That's as detailed as I can be, though you could have just taken my word and ask the admin to fix it.

Answer 1

[Mensur Dlakic]

Probably just need to remove --setupdb from your command. That switch is used to parse and process all prokka databases. Chances are you didn't mean to do that, and you likely can't write in prokka database folder anyway.