prokka

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Hi, I installed prokka and roary using conda. However, when I run the programs, they are showing the following error. Any help will be appreciated to solve the problem. Error:...

sekhwal

Argument "1.7.7" isn't numeric in numeric

18

Argument "1.7.7" isn't numeric in numeric lt (

tseemann

Databases not indexed; after indexing they *still* aren't indexed? Or are they missing?

12

When I run Prokka with: Prokka scaffolds.fasta I get this: ``` [15:34:32] This is prokka 1.14.5 [15:34:32] Written by Torsten Seemann [15:34:32] Homepage is https://github.com/tseemann/prokka [15:34:32] Local time is Thu...

wolfgangrumpf

Running prokka-genbank_to_fasta_db on new genbank format

1

Please I have been trying to setup a new genus database. I downloaded the new genbank .gbff.gz format. running prokka-genbank_to_fasta_db genomic.gbff.gz* > genome.faa genome.faa returns empty. Please how can I...

emmannaemeka

Prokka is not generating all the files while invoking prokka using shell script but working fine while running directly from commandline, why?

14

I have installed Prokka using Conda on the CentOS (7) server. Ans it is working fine when I'm invoking Prokka directly from the command line but as I want to...

Unlock-ViV

prokka-genbank_to_fasta_db error

10

Hi Seeman, I downloaded few plasmids sequences in Genbank full format from NCBI for plasmid annotation and ran the following command: `prokka ENT2_Contig6_len_41186_circ_NDM-1_Plasmid.fasta --outdir PROKKA_05222020_with_AllNDM_plasmids --proteins All_NDM_Assigned_Plasmids_byMash_Plsdb.gb ` However, I...

ramadatta

Plasmid Annotations

1

Dear tseemann, I want to only annotate plasmid sequences from an assembly file (contig.fa). Can you please guide how can i do this? Thanks J.A

Javaria-Ashraf

I face the following problem, when I used "$HOME/prokka/bin/prokka --setupdb" the database are install in "/home/hisham/prokka/db" while when i checked the list of databases I found them in "/var/lib/prokka/db" How...

H440775h

Link `--proteins` section of manual to `fasta-db-format` section

1

Hopefully addresses recurring issues that I and others have encountered (#10, #525) with taking an unnecessarily long time to find this information. I expected it to be mentioned here, but...

0xaf1f

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

19

powersequence@CH-CB-POWERSEQ:~$ prokka --help Can't locate Bio/Root/Version.pm in @INC (you may need to install the Bio::Root::Version module) (@INC contains: /home/powersequence/anaconda3/bin/../perl5 /home/powersequence/anaconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/powersequence/anaconda3/lib/site_perl/5.26.2 /home/powersequence/anaconda3/lib/5.26.2/x86_64-linux-thread-multi /home/powersequence/anaconda3/lib/5.26.2 .) at /home/powersequence/anaconda3/bin/prokka line 32. BEGIN failed--compilation...

ramnageena11