X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pipelinepdscommand.cpp;fp=pipelinepdscommand.cpp;h=2bbf2234e6a1e99cf0c15975c54eba842281fe84;hb=6a0001cc8c2f8de157f4979fd0d97a6e911b58e8;hp=691d35d84f2040c4c10dabe37990d70e90c26e1a;hpb=df41d90a9611eab75d0516e2654ed8580f8df24c;p=mothur.git

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index 691d35d..2bbf223 100644
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -375,8 +375,11 @@ bool PipelineCommand::checkForValidAndRequiredParameters(string name, string opt
 				itMade = mothurMadeFiles.find(it->first);
 				
 				if (itMade == mothurMadeFiles.end()) {  
-					m->mothurOut("You have the " + it->first + " listed as a mothurmade file for the " + name + " command, but it seems mothur will not make that file in your current pipeline, please correct."); m->mothurOutEndLine();
-					return true;
+					if ((name == "align.seqs") && (it->first == "candidate")) {} //do nothing about candidate
+					else {
+						m->mothurOut("You have the " + it->first + " listed as a mothurmade file for the " + name + " command, but it seems mothur will not make that file in your current pipeline, please correct."); m->mothurOutEndLine();
+						return true;
+					}
 				}
 			}
 		}