X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.cpp;h=e2b93316a4ade033f6ce4db3988cfd09cbf432e9;hb=ffc44592ff7ae94f14f9e21f87198e33d323cd1d;hp=8647e7510088014e48153f33a81fec8fd62ee64e;hpb=43ed0accfbc2852849e104ff7eccdd2c42acd4ec;p=mothur.git

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 8647e75..e2b9331 100644
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -633,6 +633,7 @@ int ChimeraSlayerCommand::execute(){
 #endif
 				
 				totalChimeras = deconvoluteResults(parser, outputFileName, accnosFileName, trimFastaFileName);
+                m->mothurOutEndLine(); m->mothurOut(toString(totalChimeras) + " chimera found."); m->mothurOutEndLine();
 #ifdef USE_MPI	
 				}
 				MPI_Barrier(MPI_COMM_WORLD); //make everyone wait
@@ -641,7 +642,7 @@ int ChimeraSlayerCommand::execute(){
 	
 			if (parser != NULL) { delete parser; } 
 			
-			m->mothurOutEndLine(); m->mothurOut(toString(totalChimeras) + " chimera found."); m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences.");	m->mothurOutEndLine();
+            m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences.");	m->mothurOutEndLine();
 		}
 		
 		//set accnos file as new current accnosfile
@@ -1158,14 +1159,15 @@ string ChimeraSlayerCommand::getNamesFile(string& inputFile){
 		string inputString = "fasta=" + inputFile;
 		m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
 		m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine(); 
-		
+		m->mothurCalling = true;
+        
 		Command* uniqueCommand = new DeconvoluteCommand(inputString);
 		uniqueCommand->execute();
 		
 		map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 		
 		delete uniqueCommand;
-		
+		m->mothurCalling = false;
 		m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
 		
 		nameFile = filenames["name"][0];