Ensure kmc honours RAM list

tseemann · Mar 13, 2020 · 62c9f5a · 62c9f5a
1 parent 8b64730
commit 62c9f5a
Showing 1 changed file with 1 addition and 1 deletion.
diff --git 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);