X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pipelinepdscommand.cpp;h=22f5a97b498187b23b651695e8b3d9a1b8cef1f6;hb=8f909cf6870cc2e4d8ed8cff69a203f6f83a160b;hp=26969d81c7b6d95a0f7c603489be1da984ea7d99;hpb=672cc1adbb2f8dac82757653cd579c093fe886c2;p=mothur.git

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index 26969d8..22f5a97 100644
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -238,6 +238,8 @@ int PipelineCommand::execute(){
 	try {
 		if (abort == true) { return 0; }
 		
+		int start = time(NULL);
+		
 		if (pipeFilename == "") { 
 			createPatsPipeline(); 
 			
@@ -279,6 +281,8 @@ int PipelineCommand::execute(){
 		
 		if (m->control_pressed) { return 0; }
 		
+		m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run the pipeline analysis."); m->mothurOutEndLine(); m->mothurOutEndLine();
+		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}
@@ -595,33 +599,33 @@ void PipelineCommand::createPatsPipeline(){
 		//trim.seqs command
 		string fastaFile = m->getRootName(m->getSimpleName(sffFile)) + "fasta";
 		string qualFile = m->getRootName(m->getSimpleName(sffFile)) + "qual";
-		//thisCommand = "trim.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", allfiles=F, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, oligos=" + oligosFile + ", qfile=" + qualFile + ")";
+		//thisCommand = "trim.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", allfiles=T, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, oligos=" + oligosFile + ", qfile=" + qualFile + ")";
 		//commands.push_back(thisCommand);
 		
 		//unique.seqs
 		string groupFile = m->getRootName(m->getSimpleName(fastaFile)) + "groups";
 		qualFile =  m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
 		fastaFile =  m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";
-		//thisCommand = "unique.seqs(fasta=" + fastaFile + ")"; 
-		//commands.push_back(thisCommand);
+		thisCommand = "unique.seqs(fasta=" + fastaFile + ")"; 
+		commands.push_back(thisCommand);
 		
 		//align.seqs
 		string nameFile = m->getRootName(m->getSimpleName(fastaFile)) + "names";
 		fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "unique" + m->getExtension(fastaFile);
-		//thisCommand = "align.seqs(processors=" + toString(processors) + ", candidate=" + fastaFile + ", template=" + alignFile + ")";
-		//commands.push_back(thisCommand);
+		thisCommand = "align.seqs(processors=" + toString(processors) + ", candidate=" + fastaFile + ", template=" + alignFile + ")";
+		commands.push_back(thisCommand);
 		
 		//screen.seqs
 		fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "align";
-		//thisCommand = "screen.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", name=" + nameFile + ", group=" + groupFile + ", optimize=end-minlength)";
-	//	commands.push_back(thisCommand);
+		thisCommand = "screen.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", name=" + nameFile + ", group=" + groupFile + ", optimize=end-minlength)";
+		commands.push_back(thisCommand);
 		
 		//chimera.slayer
 		fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "good" + m->getExtension(fastaFile);
 		nameFile = m->getRootName(m->getSimpleName(nameFile)) + "good" + m->getExtension(nameFile);
 		groupFile = m->getRootName(m->getSimpleName(groupFile)) + "good" + m->getExtension(groupFile);
-		//thisCommand = "chimera.slayer(processors=" + toString(processors) + ", fasta=" + fastaFile + ", template=" + chimeraFile + ")";
-	//	commands.push_back(thisCommand);
+		thisCommand = "chimera.slayer(processors=" + toString(processors) + ", fasta=" + fastaFile + ", template=" + chimeraFile + ")";
+		commands.push_back(thisCommand);
 		
 		//remove.seqs
 		string accnosFile = m->getRootName(m->getSimpleName(fastaFile))  + "slayer.accnos";