fixed bug in make.biom that occurred if some taxonomies had confidence scores and...

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index a086c987b9a29711a25e95e64953023df7deaa0f..508e2a90610d1b3705972a976580d90937358427 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -136,7 +136,7 @@ ShhherCommand::ShhherCommand(string option) {
                        flowFileName = validParameter.validFile(parameters, "flow", true);
                        flowFilesFileName = validParameter.validFile(parameters, "file", true);
                        if (flowFileName == "not found" && flowFilesFileName == "not found") {
-                               m->mothurOut("values for either flow or file must be provided for the shhh.seqs command.");
+                               m->mothurOut("values for either flow or file must be provided for the shhh.flows command.");
                                m->mothurOutEndLine();
                                abort = true; 
                        }
@@ -431,6 +431,8 @@ int ShhherCommand::execute(){
                                
                                if (m->control_pressed) { break; }
                                
+                
+                
                                getOTUData(listFileName);
 
                                m->mothurRemove(distFileName);
@@ -443,6 +445,7 @@ int ShhherCommand::execute(){
 
                                if (m->control_pressed) { break; }
                                
+            
                                for(int i=1;i<ncpus;i++){
                                        MPI_Send(&numOTUs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
                                        MPI_Send(&singleLookUp[0], singleLookUp.size(), MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
@@ -2448,7 +2451,7 @@ int ShhherCommand::cluster(string filename, string distFileName, string namesFil
                NameAssignment* clusterNameMap = new NameAssignment(namesFileName);
                clusterNameMap->readMap();
                read->read(clusterNameMap);
-               
+        
                ListVector* list = read->getListVector();
                SparseMatrix* matrix = read->getMatrix();