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
which -a makeblastdb
? $\endgroup$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. $\endgroup$