Prokka error message
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
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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.
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Mensur Dlakic
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when I removed the
--setupdb, the following error message appearedafter that, I changed my script to
and still not working and the following error message appeared
You need to run
prokka --setupdbas 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 theCould not run command:error. You may need to ask the system admin to set up databases first.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/makeblastdbThe 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 usingmakeblastdbwhich 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.