added classify.otu command

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index eee316093d81b9385cac7ff428ed2671cf3aee1e..e5c04949905d7edd6ba5ec45f4fd5a8214053471 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -320,7 +320,7 @@ void ClassifySeqsCommand::help(){
                m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n");
                m->mothurOut("The numwanted parameter allows you to specify the number of sequence matches you want with the knn method.  The default is 10.\n");
                m->mothurOut("The cutoff parameter allows you to specify a bootstrap confidence threshold for your taxonomy.  The default is 0.\n");
-               m->mothurOut("The probs parameter shut off the bootstrapping results for the bayesian method. The default is true, meaning you want the bootstrapping to be run.\n");
+               m->mothurOut("The probs parameter shuts off the bootstrapping results for the bayesian method. The default is true, meaning you want the bootstrapping to be shown.\n");
                m->mothurOut("The iters parameter allows you to specify how many iterations to do when calculating the bootstrap confidence score for your taxonomy with the bayesian method.  The default is 100.\n");
                m->mothurOut("The classify.seqs command should be in the following format: \n");
                m->mothurOut("classify.seqs(template=yourTemplateFile, fasta=yourFastaFile, method=yourClassificationMethod, search=yourSearchmethod, ksize=yourKmerSize, taxonomy=yourTaxonomyFile, processors=yourProcessors) \n");
@@ -635,7 +635,7 @@ int ClassifySeqsCommand::execute(){
                        rename(unclass.c_str(), newTaxonomyFile.c_str());
                        
                        m->mothurOutEndLine();
-                       m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for  " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
+                       m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
                        
                        #ifdef USE_MPI  
                                }