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Hello Prokka team,
I have been using Prokka with a default setting for annotating E. coli genomes. I noticed that the identified virulence factor genes are different between ABRicate (VFDB) and Prok…
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I am running a pan-genome analysis using several Prokka annotated genomes and comparing them to complete genomes in the RefSeq database. The analysis works perfectly, however, in the output file the g…
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here is my error message:
```
[23:55:15] Looking for 'minced' - found /usr/local/bin/minced
Error: A JNI error has occurred, please check your installation and try again
Exception in thread "mai…
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egrep "COG[0-9]{4}" PROKKA_${date}.gff | cut -f9 | cut -f1,5 -d ';'| sed 's/ID=//g'| sed 's/;dbxref=COG:/\t/g' | grep COG
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Bart Ailey wrote:
The documentation is good but I could not find out how to update the default databases it runs on. Especially the HMM databases. I read about the adding the databases and found the …
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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 --ou…
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Hello @tseemann team:
I am new to prokka. I set up prokka on our HPC cluster.
after the installation, /risapps/noarch/prokka/1.14.6 is my git clone location, run
$ /risapps/noarch/prokka/1.14…
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- [x] amos https://github.com/Homebrew/homebrew-science/pull/6135
- [ ] graphlan
- [ ] maker
- [ ] mlst
- [ ] prokka
- [ ] velvetoptimiser
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Running: prodigal -i PROKKA_04122024\/PROKKA_04122024\.fna -c -m -g 11 -p single -f sco -q
[19:56:37] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:224958..225212 on + strand
[19:5…
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I installed through git clone https://github.com/eead-csic-compbio/metagenome_Pfam_score
I installed HMMER v3.1b2 and all the dependencies through conda
numpy
matplotlib
pandas
seaborn
Im …