X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deconvolutecommand.cpp;h=ec809730a036245f34dfc2bc0331b108c5d10b38;hb=60928795782d8f8648ec373d6a96b53032a77429;hp=51fa43b39f87f06a3054808acb4937e05ae2337f;hpb=372fb21ea66ced432b109225851a1b80ef0491a3;p=mothur.git

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 51fa43b..ec80973 100644
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -209,7 +209,7 @@ int DeconvoluteCommand::execute() {
         }
         CountTable ct;
         if (countfile != "")  {  
-            ct.readTable(countfile, true);
+            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();	}