X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=shhhercommand.cpp;h=19ffc899d60ac778ac4eedbeb2034a62b5e04bd7;hb=e10c72304ee071c0c40e0218a06d89dc4731cbc2;hp=fe0685bea19678213fa0ddb8ccfade9ad08c4b12;hpb=f509429e06e545bde69c97cacc0eb436775bd329;p=mothur.git

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index fe0685b..19ffc89 100644
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -1931,7 +1931,7 @@ void ShhherCommand::writeClusters(vector<int> otuCounts){
 
 int ShhherCommand::execute(){
 	try {
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		getSingleLookUp();	if (m->control_pressed) { return 0; }
 		getJointLookUp();	if (m->control_pressed) { return 0; }