`$prodigal_mode` is always single

[Q-Bach]

prokka/bin/prokka

Line 727 in 045d3c5

my $prodigal_mode = ($totalbp >= 100000 && !$metagenome) || defined $prodigaltf ? 'single' : 'meta';

prokka/bin/prokka

Line 1771 in 045d3c5

{OPT=>"prodigaltf=s", VAR=>\$prodigaltf, DEFAULT=>'', DESC=>"Prodigal training file" },

Since $prodigaltf is always defined as empty string, $prodigal_mode will always evaluate to single mode of prodigal, never to meta mode.

[ucabuk]

Yes ! Indeed, I compared compared the prokka --metagenome and prodigal -p meta mode, and the outputs are different. Prokka truncated the proteins because of probably single mode. Anyone trying this needs to be aware of that!