diff --git a/tools/cd-hit/Snakefile b/tools/cd-hit/Snakefile
index e023f862fd424c5387ad06b42b76b818bc011791..583a736890ce2835401ee636b7d4ac84e450d4ec 100644
--- a/tools/cd-hit/Snakefile
+++ b/tools/cd-hit/Snakefile
@@ -105,5 +105,5 @@ rule cd_hit:
         command = []
         if params.modules:
         	command.append("module load {params.modules}")
-        command.append("{params.exec_command} {params.options} -i {input} -T {threads} -o {output}")
+        command.append("{params.exec_command} {params.options} -i {input} -T {threads} -M 0 -o {output}")
         shell(" && ".join(command))