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.
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.