X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deconvolutecommand.cpp;h=ec809730a036245f34dfc2bc0331b108c5d10b38;hb=HEAD;hp=8b73425fc5c2aefb2d7e3b4a87caf4fa8be44c40;hpb=af0a94ea8f02421b2b73e77e68753a2b4c37768e;p=mothur.git

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 8b73425..ec80973 100644
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -209,7 +209,7 @@ int DeconvoluteCommand::execute() {
         }
         CountTable ct;
         if (countfile != "")  {  
-            ct.readTable(countfile, false);
+            ct.readTable(countfile, true, false);
             if (countfile == outCountFile){
                 //prepare filenames and open files
                 map<string, string> mvariables;
@@ -286,7 +286,7 @@ int DeconvoluteCommand::execute() {
 			
 			m->gobble(in);
 			
-			if(count % 1000 == 0)	{ m->mothurOut(toString(count) + "\t" + toString(sequenceStrings.size())); m->mothurOutEndLine();	}
+			if(count % 1000 == 0)	{ m->mothurOutJustToScreen(toString(count) + "\t" + toString(sequenceStrings.size()) + "\n");	}
 		}
 		
 		if(count % 1000 != 0)	{ m->mothurOut(toString(count) + "\t" + toString(sequenceStrings.size())); m->mothurOutEndLine();	}