X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.cpp;h=65b5956cce5c0a6418d5d9524218b35b0b335aa8;hb=dfa69e4bbb18b2313495822f36b80cb475b7fb08;hp=30dda1f68518bf395ae0cbb892cf71a3a7ded4d5;hpb=134a9c1275862a6b3ea10a2c0f11965c0a535854;p=mothur.git

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 30dda1f..65b5956 100644
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -267,7 +267,7 @@ int ScreenSeqsCommand::execute(){
 		int start = time(NULL);
 		
 #ifdef USE_MPI	
-			int pid, end, numSeqsPerProcessor; 
+			int pid, numSeqsPerProcessor; 
 			int tag = 2001;
 			vector<unsigned long int> MPIPos;
 			
@@ -507,13 +507,13 @@ int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 		outputNames.push_back(goodNameFile);  outputTypes["name"].push_back(goodNameFile);
 		
 		ofstream goodNameOut;	m->openOutputFile(goodNameFile, goodNameOut);
-	
+		
 		while(!inputNames.eof()){
 			if (m->control_pressed) { goodNameOut.close();  inputNames.close(); remove(goodNameFile.c_str());  return 0; }
 
 			inputNames >> seqName >> seqList;
 			it = badSeqNames.find(seqName);
-			
+				
 			if(it != badSeqNames.end()){
 				badSeqNames.erase(it);
 				
@@ -558,7 +558,7 @@ int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 				if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodNameFile.c_str());  remove(goodGroupFile.c_str()); return 0; }
 
 				inputGroups >> seqName >> group;
-
+				
 				it = badSeqGroups.find(seqName);
 				
 				if(it != badSeqGroups.end()){
@@ -580,7 +580,8 @@ int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 				}
 			}
 		}
-			
+		
+		
 		return 0;
 	
 	}
@@ -721,7 +722,11 @@ int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition,
 				out.close();
 				
 				exit(0);
-			}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+			}else { 
+				m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+				for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+				exit(0);
+			}
 		}
 		
 		num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
@@ -1046,7 +1051,11 @@ int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, st
 				out.close();
 				
 				exit(0);
-			}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+			}else { 
+				m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+				for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+				exit(0);
+			}
 		}
 		
 		//force parent to wait until all the processes are done