Prodigal: don't set metagenome mode if training file given

[jvolkening]

Currently, when running prodigal, prokka automatically sets anonymous (formerly metagenome) mode when the total input sequences are shorter than 100,000 bases. If a training file is specified with the --prodigaltf option, it is ignored by prodigal because of this.

The current patch changes the behavior to not set anonymous mode if a training file is specified, regardless of input length. It also adds a check to make sure the prodigal file is readable, and croaks if not (currently this is silently ignored).