1.22.0

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 3b7b4a8c595cfeb9d6149a05a2b5347e6adfe6cc..af6d91449065af894f086c497cfcbc171f374098 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -376,12 +376,16 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                        temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
                        convert(temp, kmerSize); 
                        
+                       temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
+                       m->setProcessors(temp);
+                       convert(temp, processors); 
+                       
                        temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
                        save = m->isTrue(temp); 
                        //this is so the threads can quickly load the reference data
                        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                        #else
-                       if (processors != 1) { save = true; }
+                       if ((processors != 1) && (rdb->referenceSeqs.size() == 0)) { save = true; }
                        #endif
                        rdb->save = save; 
                        if (save) { //clear out old references
@@ -416,10 +420,6 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                        }else if (taxonomyFileName == "not open") { abort = true; }     
                        else {  if (save) {     rdb->setSavedTaxonomy(taxonomyFileName);        }       }
                        
-                       temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
-                       m->setProcessors(temp);
-                       convert(temp, processors); 
-                       
                        search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
                        
                        method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "bayesian";    }