How can I build custom Prokka database?

Question

[eennadi]

Please does anyone know how I can build a custom Prokka database particularly for the Caudovirales?

I want to be able to

say Prokka --usegenus --genus Caudovirales.

Thanks

Answer 1

[patrickdm]

Hello, this is how I build a custom Prokka DB i.e. for genus Bacillus:

Download all the available assemblies for genus Bacillus from NCBI (GenBank, Genomic GenBank format); uncompress the downloaded package then in the resulting assemblies folder run:

$ gunzip *.gz

$ prokka-genbank_to_fasta_db *.gbff > Bacillus.faa

$ cdhit -i Bacillus.faa -o Bacillus -T 0 -M 0 -g 1 -s 0.8 -c 0.9

$ makeblastdb -dbtype prot -in Bacillus

$ mv Bacillus Bacillus.p?? <your-path-to>/prokka/db/genus/

$ prokka --setupdb

Hth, and Happy 2022!

[Mensur Dlakic]

I think instead of

mv Bacillus ~/prokka/db/genus/

it should be

mv Bacillus Bacillus.p?? ~/prokka/db/genus/

This is also assuming that prokka is installed in one's home directory, which certainly does not hold universally. That means one may have to enter the actual location of prokka directory instead of ~/prokka

[patrickdm]

Yes, it is assuming that prokka is instalIed in home, and the path should adjusted to the actual prokka/db/genus path. I also agree with your second point. I'll edit my previous aswer accordingly.

Thank you for the clarification.

Answer 2

[eennadi]

Thanks for the reply.

I have a number of .gbff.gz files. so I ran

prokka-genbank_to_fasta_db *.gbff.gz > sample.faa

or prokka-genbank_to_fasta_db GCF_* > sample.faa

But sample.faa is empty.

What is the best command line to get prokka-genbank_to_fasta_db*.gbff.gz > sample.faa to work?

Thanks

[Mensur Dlakic]

The command most likely doesn't work with gzipped files. You may need to do this first:

gunzip *.gbff.gz

That command will unpack the files and remove the .gz extension from them. After that a slightly modified command (no .gz) should work:

prokka-genbank_to_fasta_db *.gbff > sample.faa