Prokka only creates .log file


Hi everyone.
I'm using prokka for the first time. I just installed the program using conda, I installed it in an environment with programs like trimmomatic and fastqc.

I runned prokka contigs.fa --kingdom Viruses --rfam and then a directory was created. When I opened it there was only one file: PROKKA_XXXXXXXX.log, the .faa, .gbk, .gff, .txt and .fna are missing. What could be the problem?

I was following the commands that the teacher gave us, so the command is not the problem since it worked for him.






Insufficient information. What was the screen output? What was in the log file?

A correct way of running prokka, using your example, would be:

prokka --kingdom Viruses --rfam contigs.fa

By this I mean that fasta file comes at the end. Even before that, one has to download and install HMM databases - don't know if conda takes care of it because I don't use it - and prokka must perform a database setup by indexing all available databases.

prokka --setupdb

Prokka's github page should have information about downloading and installing databases.

before adding your answer.

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