X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.cpp;h=fc98c10924138a3aa168dabbc609f64bfb89f3e4;hb=79ca496859f48f1c38803c0f7c603faac348fe4c;hp=a871244f4538881c8d285c2a1202597be319498d;hpb=7a18f1438113f6c52c66f97ae0044cfa365dd221;p=mothur.git

diff --git a/aligncommand.cpp b/aligncommand.cpp
index a871244..fc98c10 100644
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -965,6 +965,9 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
 		
 		//Close all thread handles and free memory allocations.
 		for(int i=0; i < pDataArray.size(); i++){
+            if (pDataArray[i]->count != pDataArray[i]->end) {
+                m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; 
+            }
 			num += pDataArray[i]->count;
 			CloseHandle(hThreadArray[i]);
 			delete pDataArray[i];