prokka

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Report Bug on WSL Ubuntu

1

The sequences have not been indexed. Please run "prokka --setupdb" first.  i'm pretty sure the database is installed but idk what this means...

ruqaiyatasneem

prokka not giving out put if sequence is submitted

2

prokka --cpus 4 --prefix GENE --kingdom Bacteria --locustag GENE genome.fas [13:17:11] This is prokka 1.14.5 [13:17:11] Written by Torsten Seemann [13:17:11] Homepage is https://github.com/tseemann/prokka [13:17:11] Local time is Thu Feb...

willownine

Please rename your contigs or use --centre XXX to generate clean contig names

9

So I just tried prokka on a file that contained one sequence as such: ``` >contig00001 length=455937 numreads=17237 AACTAACAACTAACAACCAACAACAAACCACTAACACATTTGTCTTTCTACAGCCGCTGG ATCTTTCCCTATTTGATGGATATTGCGATGCGAGATTCGTTGTTCACGCGTCATCGGGTC GGATTGCTGTCTGCTGTGAGGGGGGATGTGTTGGAAATCGGAGTCGGTACCGGATTGAAT TTGAAGCATTATCCTGAGCAGACGACGCGGCTCAATGTAGTGGATTCCAATCCTGGAATG AACGTGCTTCTGCGTCGCCGCATGAAGGGTATTCCATTTCCTGTGCAGCATGCCACAATC ``` The command: ``` ~/programs/prokka111/bin/prokka --outdir output...

xapple

Hello prokka developers, I am experimenting with different genetic codes for prophage sequences. I tried genetic code 4 and 11, works fine. Maybe for genetic code 4, I saw warnings...

ZarulHanifah

I run prokka with different options, but when I run the analysis of a 4.6Mba genome, about 10000 CDS are identified and the closest genome has 4600 CDS, what can...

adolfoisla

Since the development, NCBI libraries was updating 'tbl2asn' and then they changed the library name to 'table2asn'. It is been so long since prokka has been updated and there is...

ahm3draxa

Prokka Stopped: Cannot call method next result

1

I was running Prokka and this error came up...any insight as to the challenge? Thanks! STACK Bio::SearchIO::_load_format_module /home/user/miniconda3/lib/perl5/site_perl/Bio/SearchIO.pm:619 STACK Bio::SearchIO::new /home/user/miniconda3/lib/perl5/site_perl/Bio/SearchIO.pm:217 STACK toplevel /home/user/miniconda3/bin/prokka:1030 ------------------------------------- For more information about the...

KFWins2022

I'm getting the error below when I try to recreate conda (mamba) environments from yaml files if they contain prokka (example attached [saved as TXT]). I've tested for different envs...

JPegorino

Hello, I am a beginner in bioinformatics field. I tried to use prokka and I have the following problem: [19:13:48] Looking for 'signalp' - found /export/apps/bin/signalp [19:13:48] Coult not parse...

JCSigala

Could not determine version of tbl2asn - please install version 24.3 or higher

3

Hi, I installed prokka use git, and when I execute "prokka assembly.fasta --force", I met the problem above. Then I reinstalled the tbl2asn from "https://ftp.ncbi.nlm.nih.gov/asn1-converters/by_program/table2asn/mac.table2asn.gz", and added to the environment...

peiyaohu