X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.cpp;h=f9c0436c62874864279e533a3258d72bf2f6cf2d;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=fc98c10924138a3aa168dabbc609f64bfb89f3e4;hpb=c85db0a4be3a1f8037a71a23ca73f9762184e28a;p=mothur.git

diff --git a/aligncommand.cpp b/aligncommand.cpp
index fc98c10..f9c0436 100644
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -644,11 +644,11 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
 			#endif
 			
 			//report progress
-			if((count) % 100 == 0){	m->mothurOut(toString(count)); m->mothurOutEndLine();		}
+			if((count) % 100 == 0){	m->mothurOutJustToScreen(toString(count) + "\n"); 		}
 			
 		}
 		//report progress
-		if((count) % 100 != 0){	m->mothurOut(toString(count)); m->mothurOutEndLine();		}
+		if((count) % 100 != 0){	m->mothurOutJustToScreen(toString(count) + "\n"); 		}
 		
 		delete alignment;
 		alignmentFile.close();