testing 1.14.0

diff --git a/mothur b/mothur
index a609d20980d33ea8c7c66e0e3de5c294e133174c..a29d1c921ddf4ac19cc9bd424dd210a8e973e05a 100755 (executable)
Binary files a/mothur and b/mothur differ

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index 691d35d84f2040c4c10dabe37990d70e90c26e1a..2bbf2234e6a1e99cf0c15975c54eba842281fe84 100644 (file)
--- 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;
+                                       }
                                }
                        }
                }