X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimerauchimecommand.cpp;h=3a9f42b22e0715ccf1f68313439342269da81bf8;hp=346afe213b12fab2baab1e4d23102e526f6ecc8c;hb=ac03f1f6c27b5bfdf2cfb6d45c3667c3e0281f51;hpb=fe08eacea5a2d34cd4bd27e8451fd2872102a80a

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 346afe2..3a9f42b 100644
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -569,6 +569,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
 
 			
 			if (hasName && (templatefile != "self")) { m->mothurOut("You have provided a namefile and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
+            if (hasCount && (templatefile != "self")) { m->mothurOut("You have provided a countfile and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
 			if (hasGroup && (templatefile != "self")) { m->mothurOut("You have provided a group file and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
 			
 			//look for uchime exe