Hello, Im using prokka to annotated my metagenomes and its stuck on this step

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[22:19:31] Generating annotation statistics file
[22:19:38] Generating Genbank and Sequin files
[22:19:38] Running: tbl2asn -V b -a r10k -l paired-ends -M b -N 1 -y 'Annotated using prokka 1.14.6 from <https://github.com/tseemann/prokka>' -Z output\/03_prokka\/MA01PA\/MA01PA\.err -i output\/03_prokka\/MA01PA\/MA01PA\.fsa 2> /dev/null

I looks like its quite common in metagenomes but I was wondering if I cancel the job at this stage all the files produce already (.faa, .ffn, .tsv ... ) can be use or they still need to be refined after tbl2asn runs? Becuase this step is only to produce the .gbk no? When I runed prokka within the #CE9MS66BS or #C02FC6VFQG1 pipeline I didnt have this issue, do you know why or how can I solve it ??

I know that Prokka is bad at very large files. In #C02FC6VFQG1 we therefore run the tool in chunks. In #CE9MS66BS I suppose it's only run on MAGs so therefore not a problem. I have no idea if the output can be used, but I think it would be best to divide up the input file and run Prokka on them. An alternative is perhaps to use Bakta instead. I don't know if this has a metagenome mode nor if it can handle large input files.

Bakta does not have a metagenome mode, I already checked... I'll check if splitting the metagenomes is an option but im not sure how you handle the continuance of the locustags then

One can provide a locus tag to Prokka, so you could just specify the same. In #C02FC6VFQG1 we just let it be what Prokka sets it to.

The developer recommends to comment out the lines that belong to this part in the original code, in case you want to do it in a future version of #C02FC6VFQG1 but since I work on a cluster I dont know if I can do it

Actually, my tip to specify a locus tag won't work of course since that would give different features the same identifier. I didn't think of that. I don't see any drawbacks of having different locus tags so, unless you can give me some good reason, I think we'll just keep it as it is.

Im going to try bakta because I just saw that they do have a -meta option although it only affect the prodigal prediction; im unsure of what the results of that would be

Annotation in chunks is also convenient with https://github.com/qbic-pipelines/metagenomeannotation