From 5b5004436669e09189bac52de1efe4f7f2da2555 Mon Sep 17 00:00:00 2001
From: le-marquis <malte.ruehlemann@gmail.com>
Date: Wed, 15 Nov 2017 11:28:02 +0100
Subject: [PATCH] Use GNU-parallel to run prodigal faster

---
 bin/prokka | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/prokka b/bin/prokka
index 5c7ef02..98c8291 100755
--- a/bin/prokka
+++ b/bin/prokka
@@ -703,7 +703,7 @@ 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 $cmd = "cat \Q$outdir/$prefix.fna\E | parallel -j $cpus --block 100k --recstart '>' --pipe prodigal -c -m -g $gcode -p $prodigal_mode -f sco -q";
 msg("Running: $cmd");
 open my $PRODIGAL, '-|', $cmd;
 my $sid;