From 62c9f5a344d55a6a5ce584aa3842efdc3a34f821 Mon Sep 17 00:00:00 2001
From: Torsten Seemann <torsten.seemann@gmail.com>
Date: Fri, 13 Mar 2020 16:35:05 +1100
Subject: [PATCH] Ensure kmc honours RAM list

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

diff --git a/bin/shovill b/bin/shovill
index a821cd0..5d36799 100755
--- a/bin/shovill
+++ b/bin/shovill
@@ -147,7 +147,7 @@ unless ($gsize) {
   my($bp) = grep { m/Estimated genome size/i } read_lines($LOGFILE);
 
   # @@@ KMC @@@
-  run_cmd("kmc -t$cpus -k$kmer -ci$minkc \Q$R1\E $tmpout/kmc $tmpout");
+  run_cmd("kmc -sm -m$half_ram -t$cpus -k$kmer -ci$minkc \Q$R1\E $tmpout/kmc $tmpout");
   unlink <$tmpout/kmc.*>;
   # No. of unique counted k-mers       :      2054586
   my($bp) = grep { m/unique counted k/i } read_lines($LOGFILE);