Allow genes to run off contig edges.

EnvGen · Apr 29, 2015 · f93751b · f93751b
1 parent b57be69
commit f93751b
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/bin/prokka b/bin/prokka
@@ -667,7 +667,7 @@ my $totalbp = sum( map { $seq{$_}{DNA}->length } @seq);
 my $prodigal_mode = ($totalbp >= 100000 && !$metagenome) ? 'single' : 'meta';
 msg("Contigs total $totalbp bp, so using $prodigal_mode mode");
 my $num_cds=0;
-my $cmd = "prodigal -i \Q$outdir/$prefix.fna\E -c -m -g $gcode -p $prodigal_mode -f sco -q";
+my $cmd = "prodigal -i \Q$outdir/$prefix.fna\E -m -g $gcode -p $prodigal_mode -f sco -q";
 msg("Running: $cmd");
 open my $PRODIGAL, '-|', $cmd;
 my $sid;