Using prodigal-gv results as input to pharokka

[Fazel-AVB]

I have run Prodigal-gv on my genomes separately with default parameters and using meta.
Can the predicted ORF files (.faa) be given directly to the Pharokka instead of running it from scratch with Fasta files?

[gbouras13]

Hi @Fazel-AVB

Yes - you can use pharokka_proteins.py. Let me know if you have any trouble.

George

[Fazel-AVB]

Hi George,
thank you for your reply.
This is the command I am using to run the pharokka_proteins.py for one of my protein files: pharokka_proteins.py -i PATH_TO_INPUT/1_ORFs.faa -o PATH_TO_OUTPUT/annotated_genomes_pharokka -d PATH_TO_DB/pharokka_db/pharokka_v1.4.0_databases -t 4 -f

However, it says the Dnaapler version is wrong!

my pharokka's version is 1.6.1.

Looking at the release history I couldn't find any recommendation regarding the version of the compatible dnaapler.

[gbouras13]

Hi @Fazel-AVB ,

I'd recommend upgrading pharokka to v1.7.4 (the latest version) - v1.6.1 is a year old now. Alternatively, you can downgrade dnaapler to v0.7.3 (or any version below v1) which should fix the issue too.

George

[Fazel-AVB]

Hi George,
Thank you for the reply. Now I was wondering if you could give a hint on how to generate gbk files using protein input.
I need these files for plotting reasons and also running Phold.

I found in post_processing.py module that for gbk creation first create_gff function should be run which receives merged_df and length_df as inputs. I think merge-df is equal to the full_merged_out file resulting from pharokka_proteins.py, right?

[gbouras13]

Hi @Fazel-AVB - you can’t really make genbank files from protein input, you will need the original contigs. If you want a genbank from pharokka, just start with the original contigs and run pharokka like normal.

george