fixes while testing

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 8a229e3cade2cff57569e16b0e4b682d8dd0be65..624aab439855f60d9072889ae2cd80b33dae320e 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -64,6 +64,7 @@ vector<string> AlignCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 AlignCommand::AlignCommand(){  
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;