prokka

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The **tranposase** in **The Core (BLAST+) Databases section** ([https://github.com/tseemann/prokka#the-core-blast-databases](url)) should be **transposase**

clf-bio

Hi, Before I begin, thanks for the wonderful pipeline! Without Prokka I wouldn't be able to study half the things I'm doing right now. Prokka annotation of our lab's Haloarchaeal...

naturepoker

Hi, I am trying to use prokka to annotate a bacteriophage genome. The following command runs through `prokka phage_genome.fasta --kingdom Viruses --gcode 11` however, everything is annotated as "hypothetical protein"....

stitam

Can not run genus specific database

1

Here is my command: prokka Z10248.fasta --prefix Z10248spa --genus spa --usegenus spa [15:03:34] This is prokka 1.14.6 [15:03:34] Written by Torsten Seemann [15:03:34] Homepage is https://github.com/tseemann/prokka [15:03:34] Local time is...

Aravindphoenix

rRNA not well annotated with Barrnap

5

Hi Torsten, I noticed Barrnap doesn't annotate well rRNA. My genomes have an intergenic spacer region of 150 bp in 23S rRNA and PROKKA annotates different CDS in that region....

ireneortega

Hi, Why do I need the `.fa` file if the sequence is already is in gbff? Currently I need to unzip and convert the Genebank file before I run this...

rfarouni

Hi, I installed prokka on a Linux system through conda, and run it, then I got an error: perl: symbol lookup error: /home/liusq/perl5/lib/perl5/x86_64-linux-thread-multi/auto/Cwd/Cwd.so: undefined symbol: Perl_xs_apiversion_bootcheck I have googled this...

sql647

prokka --metagenome vs prodigal -c

5

The #--metagenome option does not result in the same behaviour as leaving out -c in the standalone prodigal version (tested with --kingdom Viruses). Is there an option to include this...

thierryjanssens

Prokka needs makeblastdb 2.2 or higher...

1

Hi, I am running prokka 1.13 with blastp 2.11 and I get this error ``` $ prokka --setupdb .... [15:22:53] Cleaning complete. [15:22:53] Looking for 'makeblastdb' - found /opt/conda/envs/metawrap-env/bin/makeblastdb [15:22:53]...

pmitev

Hi, I just accidentally found that one of the genes start with Met in faa file, however, it starts with GTG which is Val in ffn file? This confused me...

lijie04