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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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where is contigs.fa #583

Open ryao-mdanderson opened 3 years ago

ryao-mdanderson commented 3 years ago

Hello @tseemann team:

I am new to prokka. I set up prokka on our HPC cluster.

after the installation, /risapps/noarch/prokka/1.14.6 is my git clone location, run $ /risapps/noarch/prokka/1.14.6/bin/prokka contigs.fa [23:03:13] This is prokka 1.14.6 [23:03:13] Written by Torsten Seemann torsten.seemann@gmail.com [23:03:13] Homepage is https://github.com/tseemann/prokka [23:03:13] Local time is Thu Jul 29 23:03:13 2021 [23:03:13] You are ris_hpc_apps [23:03:13] Operating system is linux [23:03:13] You have BioPerl 1.007002 [23:03:13] System has 28 cores. [23:03:13] Will use maximum of 8 cores. [23:03:13] Annotating as >>> Bacteria <<< [23:03:13] 'contigs.fa' is not a readable non-empty FASTA file

Is this as expected? where is contigs.fa? I do not find a folder PROKKA_yyyymmdd in the installation directory.

(per README

Look for a folder called PROKKA_yyyymmdd (today's date) and look at stats

% cat PROKKA_yyyymmdd/*.txt)

Thank you for help!

rpetit3 commented 3 years ago

Hi @ryao-mdanderson

The contigs.fa should be replaced with the path to the assembly FASTA file you want to annotate.