X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=secondarystructurecommand.cpp;h=26bd35444d866132fd37c34fc3e0d8fd4cf84c40;hb=191ae1be0679d5cf4eda950b3b1bf26fb7dd503d;hp=36e0f609ca67bd3cd37e7c0d33a98e88cee65e6f;hpb=fc9bc621a09de13eb76ca4f5cee930b03de43dcd;p=mothur.git

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index 36e0f60..26bd354 100644
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -25,6 +25,7 @@ vector<string> AlignCheckCommand::getValidParameters(){
 //**********************************************************************************************************************
 AlignCheckCommand::AlignCheckCommand(){	
 	try {
+		abort = true;
 		//initialize outputTypes
 		vector<string> tempOutNames;
 		outputTypes["aligncheck"] = tempOutNames;