prokka

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Hi everyone, I'm trying to create a local (custom) database for prokka based on a multifasta file that contains a set of DNA sequences of different bacterial genes. It looks...

Felipedb02

I am using Prokka to annotate a Salmonella enterica genome, and I used the --proteins option to provide the S. enterica LT2 reference genome in .gbf format. Unnamed genes in...

ReganDM

prokka setup db

2

Hallo. Can you help me? anna@anna-G3-3590:~$ prokka Name: Prokka 1.14.5 by Torsten Seemann Synopsis: rapid bacterial genome annotation Usage: prokka [options] General: --help This help --version Print version and exit...

annavet

bioperl v1.7.8 kills the prokka 🐿🔫

1

Prokka checks for bioperl >= `1.0006002` numerically using this code on line 257. ``` my $minbpver = "1.006002"; # for Bio::SearchIO::hmmer3 my $bpver = $Bio::Root::Version::VERSION; msg("You have BioPerl $bpver"); err("Please...

lskatz

Hello, I wanted to know how to get another genus for Prokka, or how can I make a genus for prokka. I am working with Legionella, and I want to...

EllistonV

fangbz 23:20:10 /ldata/fangbz/software/signalp-4.1 $ which prokka /mdata/fangbz/anaconda2/bin/prokka fangbz 23:26:43 /ldata/fangbz/software/signalp-4.1 $ which signalp alias signalp='/ldata/fangbz/software/signalp-4.1/signalp' /ldata/fangbz/software/signalp-4.1/signalp fangbz 23:26:56 /ldata/fangbz/software/signalp-4.1 $ fangbz 23:27:35 /ldata/fangbz/software/signalp-4.1 $ prokka /ldata/fangbz/gl/BK124/single/bins.1.fa --outdir /ldata/fangbz/gl/BK124/single/prokka --prefix BK124...

Gao-Lei-Xinjiang

Add information about plasmid annotation

9

For plasmid you will not get a good result if you just use the default settings. I would recommend getting GENBANK files (.gbk or .gb) of all the plasmids that...

tseemann

Issue after conda install: Can't locate Bio/Root/Version.pm in @INC (you may need to install the Bio::Root::Version module)

23

Started an AWS Ubunutu 18.04 server. Installed python. Installed miniconda. Ran `conda install -c conda-forge -c bioconda -c defaults prokka` No apparent issues with install. Try running `prokka` Output: Can't...

c-leber

Hello! I used prokka for annotation of a genome. Here is my command: `prokka 1.fna --addgenes --addmrna --cpus 16 --genus Wolbachia --usegenus --species pipientis --strain wMelCS` It yields the well-known...

Yasana1990

Hi, I wonder if its possible to download the databases in a different location from where Prokka would be installed? I am using Conda Is it enough if I just...

Bibi888