fixed shhh.flows outputdir bug

[mothur.git] / preclustercommand.cpp

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index 58fd99777a809afd6384861b4a3237218138c29f..f2fbc80088b1adf2927ee78d5b1e02fbf9691cb1 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -217,17 +217,19 @@ int PreClusterCommand::execute(){
                        m->mothurOutEndLine(); 
                        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(); 
                        
                        m->renameFile(filenames["fasta"][0], newFastaFile);
+            m->renameFile(filenames["name"][0], newNamesFile);
                        
                        m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run pre.cluster."); m->mothurOutEndLine(); 
                                
@@ -302,7 +304,7 @@ int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newF
                        lines.push_back(linePair(startIndex, endIndex));
                }
                
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)          
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)         
                
                //loop through and create all the processes you want
                while (process != processors) {