X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=shhhercommand.cpp;h=e970bab34f9276a680bce6e29faa9cf829684e12;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=30815a077c19ff7663d498223c49e73ddc268809;hpb=01d5a60fc5f396339acf529151fa8186ee7c1a41;p=mothur.git

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 30815a0..e970bab 100644
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -858,7 +858,7 @@ string ShhherCommand::flowDistMPI(int startSeq, int stopSeq){
 				}
 			}
 			if(i % 100 == 0){
-				m->mothurOut(toString(i) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
+				m->mothurOutJustToScreen(toString(i) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
 			}
 		}
 		
@@ -867,7 +867,7 @@ string ShhherCommand::flowDistMPI(int startSeq, int stopSeq){
 		
 		if (m->control_pressed) { return fDistFileName; }
 		
-		m->mothurOut(toString(stopSeq) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
+		m->mothurOutJustToScreen(toString(stopSeq) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
 
 		ofstream distFile(fDistFileName.c_str());
 		distFile << outStream.str();		
@@ -2236,6 +2236,8 @@ int ShhherCommand::driver(vector<string> filenames, string thisCompositeFASTAFil
             double begClock = clock();
             unsigned long long begTime;
             
+            string fileNameForOutput = filenames[i];
+            
             for (int g = 0; g < theseFlowFileNames.size(); g++) {
                 
                 string flowFileName = theseFlowFileNames[g];
@@ -2269,7 +2271,7 @@ int ShhherCommand::driver(vector<string> filenames, string thisCompositeFASTAFil
                 begTime = time(NULL);
                
                 
-                flowDistParentFork(numFlowCells, distFileName, numUniques, mapUniqueToSeq, mapSeqToUnique, lengths, flowDataPrI, flowDataIntI);	
+                flowDistParentFork(numFlowCells, distFileName, numUniques, mapUniqueToSeq, mapSeqToUnique, lengths, flowDataPrI, flowDataIntI);
                 
                 m->mothurOutEndLine();
                 m->mothurOut("Total time: " + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/CLOCKS_PER_SEC) + '\n');
@@ -2434,7 +2436,7 @@ int ShhherCommand::driver(vector<string> filenames, string thisCompositeFASTAFil
 			}
             
             numCompleted++;
-			m->mothurOut("Total time to process " + flowFileName + ":\t" + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/(double)CLOCKS_PER_SEC) + '\n');
+			m->mothurOut("Total time to process " + fileNameForOutput + ":\t" + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/(double)CLOCKS_PER_SEC) + '\n');
 		}
 		
         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
@@ -2543,9 +2545,8 @@ int ShhherCommand::flowDistParentFork(int numFlowCells, string distFileName, int
 				}
 			}
 			if(i % 100 == 0){
-				m->mothurOut(toString(i) + "\t" + toString(time(NULL) - begTime));
-				m->mothurOut("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC));
-				m->mothurOutEndLine();
+				m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - begTime));
+				m->mothurOutJustToScreen("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC)+"\n");
 			}
 		}
 		
@@ -2555,9 +2556,8 @@ int ShhherCommand::flowDistParentFork(int numFlowCells, string distFileName, int
 		
 		if (m->control_pressed) {}
 		else {
-			m->mothurOut(toString(stopSeq-1) + "\t" + toString(time(NULL) - begTime));
-			m->mothurOut("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC));
-			m->mothurOutEndLine();
+			m->mothurOutJustToScreen(toString(stopSeq-1) + "\t" + toString(time(NULL) - begTime));
+			m->mothurOutJustToScreen("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC)+"\n");
 		}
         
         return 0;