X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerauchimecommand.cpp;h=e28775f016c4e992d2d8f2d23904c93c6e3f74ef;hb=0c64d4590ecba2cb19475ca0af206d85bfb2195c;hp=026e91b01f188ce180c3b645de8451138efe0e02;hpb=72e0be6b9c80009d4dbee24e8d690ad9514dc6fb;p=mothur.git

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 026e91b..e28775f 100644
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -12,7 +12,7 @@
 //#include "uc.h"
 #include "sequence.hpp"
 #include "referencedb.h"
-
+#include "systemcommand.h"
 
 //**********************************************************************************************************************
 vector<string> ChimeraUchimeCommand::setParameters(){	
@@ -463,10 +463,20 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
 			string uchimeCommand;
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			uchimeCommand = path + "uchime";	//	format the database, -o option gives us the ability
+            if (m->debug) { 
+                m->mothurOut("[DEBUG]: Uchime location using \"which uchime\" = "); 
+                Command* newCommand = new SystemCommand("which uchime"); m->mothurOutEndLine();
+                newCommand->execute();
+                delete newCommand;
+                m->mothurOut("[DEBUG]: Mothur's location using \"which mothur\" = "); 
+                newCommand = new SystemCommand("which mothur"); m->mothurOutEndLine();
+                newCommand->execute();
+                delete newCommand;
+            }
 #else
 			uchimeCommand = path + "uchime.exe";
 #endif
-			
+        
 			//test to make sure uchime exists
 			ifstream in;
 			uchimeCommand = m->getFullPathName(uchimeCommand);