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I am running this in the same directory as my prokka gff files and I have 258 genomes:
roary -f roary_output -e -v --mafft -p 40 -i 70 -s -g 150000 -b "blastp num_threads 30 perc_identity = 70" *…
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Hi,
I have a .gff file that was obtained from prokka. Converting the gff file into gtf format gives me file with no output. Im not sure if im going wrong somewhere. Any help will be appreciated. I'…
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Hi, I have some bacteria genomes (Vibrio vulnificus strains), it was assembled using Spades, and then I use the generated contigs to generate a file.faa using prokka, an then I used it to generate a l…
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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 ha…
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## Is your feature request related to a problem? Please describe
Somewhat related to a problem, but also at the same time not really. I totally agree with compressed files should be use…
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Hello,
I am running the metro wrap pipeline, In the bin refinement step I got the error mentioned below, kindly help me to solve it
**----- There are 0 'good' bins found in binsA! (…
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```
❯❯❯ bedtools intersect -v -a a.gff -b b.gff
Error: line number 11752 of file a.gff has 1 fields, but 9 were expected.
```
### a.gff
```
…
38 prokka gene 981 1121 . - 1 ID=OU3MT_0587…
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@taylorreiter and @luizirber the snakefiles for downloading and calculating signatures for the ihmp IBD data are [here](https://github.com/dib-lab/2017-paper-gather/tree/ihmp/ihmp/snakefile) on the ih…
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Hello
I am trying to install prokka on my new mac MacOS BigSur M1. I tried just installing miniconda and installing with
conda install -c conda-forge -c bioconda -c defaults prokka
it runs thi…
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The sequences have not been indexed. Please run "prokka --setupdb" first.
![Screenshot (481)](https://github.com/tseemann/prokka/assets/153951377/b00fb2fa-c665-479c-a1e8-d10bf309a358)
i'm pretty s…