From 73c3d99bc6a88aa36073a1923f232884cf387191 Mon Sep 17 00:00:00 2001
From: "Falk Hildebrand (QIB)" <hildebra@v0768.nbi.ac.uk>
Date: Tue, 5 Sep 2023 17:21:17 +0100
Subject: [PATCH] LCAhits.log activated

---
 lotus2 | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lotus2 b/lotus2
index 4f5658b..4a505fb 100755
--- a/lotus2
+++ b/lotus2
@@ -5522,7 +5522,9 @@ sub makeAbundTable2($ $) {
         }
         my $LCxtr = "";
         if ($pseudoRefOTU) { $LCxtr = "-showHitRead -reportBestHit"; }
-        my $cmd = "$LCABin  -i " . join( ",", @blOuts ) . " -r " . join( ",", @TAX_RANKS ) . " -o $SIM_hierFile $LCxtr -LCAfrac $LCAfraction  -cover $LCAcover -minAlignLen $LCAminAliLen -id " . join( ",", @idThr ) . ";";
+		my $repHitPat = "-reportHitPattern $logDir/LCAhits.log";
+
+        my $cmd = "$LCABin  -i " . join( ",", @blOuts ) . " -r " . join( ",", @TAX_RANKS ) . " -o $SIM_hierFile $repHitPat $LCxtr -LCAfrac $LCAfraction  -cover $LCAcover -minAlignLen $LCAminAliLen -id " . join( ",", @idThr ) . ";";
 
         #die $cmd;
         if ( systemL $cmd) { printL "LCA command $cmd failed\n", 44; }