fixes while testing

[mothur.git] / secondarystructurecommand.cpp

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index 36e0f609ca67bd3cd37e7c0d33a98e88cee65e6f..26bd35444d866132fd37c34fc3e0d8fd4cf84c40 100644 (file)
--- 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;