Prokka
What does it do?
Prokka annotates genomes, letting you know what genes and other features are present. If you want to learn more about it, check out the prokka publication.
How do I use it?
Subject
In the Subject field, put Prokka. Spelling counts, but case sensitivity doesn't.
Description
All you need to put in the description is a list of SEQIDs you want to process, one per line.
Example
For an example Prokka, see issue 15195.
Interpreting Results
Prokka will output a lot of files for each genome you give it - you can find a quick description of
each file here. Of particular interest are the .gff and .gbk files.
How long does it take?
Prokka isn't the quickest thing around - expect it to take 2 to 3 minutes for each genome you give it.
What can go wrong?
- Requested SEQIDs are not available. If we can't find some of the SEQIDs that you request, you will get a warning message informing you of it.
- FTP Upload issues. Since the files prokka produces are fairly big, the need to be uploaded to an FTP site. We'll sometimes have connection issues that stop uploads from happening properly. If this is the case, you'll get a message telling you to try again later. FTP connection issues usually only persist for a few hours at a time.