X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerauchimecommand.cpp;h=01289a0d0edf66969827d65a11a703c24da86845;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=0846bbd9d1755f73e690e4bf11f72f0282fdfe25;hpb=88fbc534a92cb91900e98a3288dfa1f68828b69b;p=mothur.git

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 0846bbd..01289a0 100644
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -418,7 +418,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
 				
 			string temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);
+			m->mothurConvert(temp, processors);
 			
 			abskew = validParameter.validFile(parameters, "abskew", false);	if (abskew == "not found"){	useAbskew = false;  abskew = "1.9";	}else{  useAbskew = true;  }
 			if (useAbskew && templatefile != "self") { m->mothurOut("The abskew parameter is only valid with template=self, ignoring."); m->mothurOutEndLine(); useAbskew = false; }
@@ -987,6 +987,11 @@ int ChimeraUchimeCommand::driverGroups(SequenceParser& parser, string outputFNam
 
 int ChimeraUchimeCommand::driver(string outputFName, string filename, string accnos, string alns, int& numChimeras){
 	try {
+		
+		outputFName = m->getFullPathName(outputFName);
+		filename = m->getFullPathName(filename);
+		alns = m->getFullPathName(alns);
+		
 		//to allow for spaces in the path
 		outputFName = "\"" + outputFName + "\"";
 		filename = "\"" + filename + "\"";