added modify names parameter to set.dir

[mothur.git] / countseqscommand.cpp

diff --git a/countseqscommand.cpp b/countseqscommand.cpp
index 6afd1f47b06591d19d274ce91793edd73d4cabc7..411a814d73671ebb69b43a783e36e31d6263fe45 100644 (file)
--- a/countseqscommand.cpp
+++ b/countseqscommand.cpp
@@ -373,12 +373,13 @@ int CountSeqsCommand::createProcesses(GroupMap*& groupMap, string outputFileName
 
         
         //sanity check
-        if (numSeqs != groupMap->getNumSeqs()) {
-            m->mothurOut("[ERROR]: processes reported processing " + toString(numSeqs) + " sequences, but group file indicates you have " + toString(groupMap->getNumSeqs()) + " sequences.");
-            if (processors == 1) { m->mothurOut(" Could you have a file mismatch?\n"); }
-            else { m->mothurOut(" Either you have a file mismatch or a process failed to complete the task assigned to it.\n"); m->control_pressed = true; }
-        }
-               
+        if (groupfile != "") {
+            if (numSeqs != groupMap->getNumSeqs()) {
+                m->mothurOut("[ERROR]: processes reported processing " + toString(numSeqs) + " sequences, but group file indicates you have " + toString(groupMap->getNumSeqs()) + " sequences.");
+                if (processors == 1) { m->mothurOut(" Could you have a file mismatch?\n"); }
+                else { m->mothurOut(" Either you have a file mismatch or a process failed to complete the task assigned to it.\n"); m->control_pressed = true; }
+            }
+               }
                return numSeqs;
        }
        catch(exception& e) {