X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;fp=engine.cpp;h=ea1c0e14dc9f89fe0157d24828a2e9552297389c;hb=0ca63a8165baa0afa459e644ebe140ba496d5ba0;hp=670af78757abf5ac2b25ff2adcd4c7b41257e9ee;hpb=1b0bddfbf4ac5df7e2dad03c8a5350e71b052f78;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index 670af78..ea1c0e1 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -186,11 +186,13 @@ bool InteractEngine::getInput(){
 					mout->names.clear();
 					mout->saveNextLabel = "";
 					mout->printedHeaders = false;
+					mout->commandInputsConvertError = false;
 					mout->currentBinLabels.clear();
 					mout->binLabelsInFile.clear();
 							
 					Command* command = cFactory->getCommand(commandName, options);
-					quitCommandCalled = command->execute();
+					if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+					else { quitCommandCalled = command->execute(); }
 							
 					//if we aborted command
 					if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
@@ -370,12 +372,14 @@ bool BatchEngine::getInput(){
 					mout->names.clear();
 					mout->saveNextLabel = "";
 					mout->printedHeaders = false;
+					mout->commandInputsConvertError = false;
 					mout->currentBinLabels.clear();
 					mout->binLabelsInFile.clear();
 
 							
 					Command* command = cFactory->getCommand(commandName, options);
-					quitCommandCalled = command->execute();
+					if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+					else { quitCommandCalled = command->execute(); }
 							
 					//if we aborted command
 					if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
@@ -537,12 +541,13 @@ bool ScriptEngine::getInput(){
 					mout->names.clear();
 					mout->saveNextLabel = "";
 					mout->printedHeaders = false;
+					mout->commandInputsConvertError = false;
 					mout->currentBinLabels.clear();
 					mout->binLabelsInFile.clear();
 
-							
 					Command* command = cFactory->getCommand(commandName, options);
-					quitCommandCalled = command->execute();
+					if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+					else { quitCommandCalled = command->execute(); }
 					
 					//if we aborted command
 					if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }