X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=groupmap.cpp;fp=groupmap.cpp;h=8e2139db771010d1b372ccfdc0a6a0523c6e4849;hb=79ca496859f48f1c38803c0f7c603faac348fe4c;hp=e5d8427200aed0a61aaf04a0e7084ed0e17a0a78;hpb=b740fb182372143e152143c6cc5b9ac8591f09b7;p=mothur.git

diff --git a/groupmap.cpp b/groupmap.cpp
index e5d8427..8e2139d 100644
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -317,6 +317,10 @@ string GroupMap::getGroup(string sequenceName) {
 	if (it != groupmap.end()) { //sequence name was in group file
 		return it->second;	
 	}else {
+        //look for it in names of groups to see if the user accidently used the wrong file
+        if (m->inUsersGroups(sequenceName, namesOfGroups)) {
+            m->mothurOut("[WARNING]: Your group or design file contains a group named " + sequenceName + ".  Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine(); 
+        }
 		return "not found";
 	}
 }