added design and sets parameters to the rarefaction.shared command. finished work...

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 8647e7510088014e48153f33a81fec8fd62ee64e..e2b93316a4ade033f6ce4db3988cfd09cbf432e9 100644 (file)
--- 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];