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.
1 answer
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.
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Reading the PROKKA_XXXXXXXX.log file will likely reveal the cause of the problem.
Thank you! Turns out I need to update a package. I tried creating a new environment just for prokka and everything worked perfectly. Thank you so much.