fixes while testing

[mothur.git] / collectcommand.cpp

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 3dd2436a8a88cf21b8cd7705a799ed9ab6450ebf..9ea55b2d6068dfda14450d82d247a428dcb9ca56 100644 (file)
--- 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;