X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=collectcommand.cpp;h=9ea55b2d6068dfda14450d82d247a428dcb9ca56;hp=3dd2436a8a88cf21b8cd7705a799ed9ab6450ebf;hb=191ae1be0679d5cf4eda950b3b1bf26fb7dd503d;hpb=fc9bc621a09de13eb76ca4f5cee930b03de43dcd

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 3dd2436..9ea55b2 100644
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -72,6 +72,7 @@ vector<string> CollectCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 CollectCommand::CollectCommand(){	
 	try {
+		abort = true;
 		//initialize outputTypes
 		vector<string> tempOutNames;
 		outputTypes["sobs"] = tempOutNames;