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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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Running prokka-genbank_to_fasta_db on new genbank format #607

Open emmannaemeka opened 2 years ago

emmannaemeka commented 2 years ago

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 run prokka-genbank_to_fasta_db on the new genbank format? Thanks

kristina28 commented 2 years ago

I have successfully used seqret (from Emboss) to convert the gff files from NCBI to gbk files that I can then use with Prokka. Emboss can be installed using anaconda and then the seqret command can be something like:

seqret -sequence ref-genome.fna -feature -fformat gff -fopenfile ref-genome*.gff -osformat genbank -osname_outseq ref-genome -ofdirectory_outseq gbk_file -auto;