X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotypecommand.cpp;h=f402f2a8ab15a1808a461d376818d97d98c5c5c7;hb=a626c629e4d4840cd2ce04d98055dcfef1f8593a;hp=1d6c391de69c83a86971873577a0df0b21efdbcd;hpb=597560b3c23f03d0069082cf096ce65e0c087519;p=mothur.git

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index 1d6c391..f402f2a 100644
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -244,13 +244,15 @@ int PhylotypeCommand::execute(){
 					//make the names compatable with listvector
 					string name = "";
 					for (int i = 0; i < names.size(); i++) {  
-						if (namefile != "") {	
-							map<string, string>::iterator itNames = namemap.find(names[i]);  //make sure this name is in namefile
-		
-							if (itNames != namemap.end()) {  name += namemap[names[i]] + ",";   } //you found it in namefile
-							else { m->mothurOut(names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); exit(1);  }
-							
-						}else{   name += names[i] + ",";	}
+                        if (names[i] != "unknown") {
+                            if (namefile != "") {	
+                                map<string, string>::iterator itNames = namemap.find(names[i]);  //make sure this name is in namefile
+                                
+                                if (itNames != namemap.end()) {  name += namemap[names[i]] + ",";   } //you found it in namefile
+                                else { m->mothurOut(names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); exit(1);  }
+                                
+                            }else{   name += names[i] + ",";	}
+                        }
 					}
 					name = name.substr(0, name.length()-1);  //rip off extra ','