X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makegroupcommand.cpp;h=455826a3a8ab61ec1cf7a5af44e91ba791907583;hb=83b5acbe3d6087a6cd73e80dde4b923387a01d01;hp=57028c957397f8ead2e38cd326020391a61ef7a2;hpb=21805b1c466a341d64a5a451f156a56d12c75dca;p=mothur.git

diff --git a/makegroupcommand.cpp b/makegroupcommand.cpp
index 57028c9..455826a 100644
--- a/makegroupcommand.cpp
+++ b/makegroupcommand.cpp
@@ -60,18 +60,26 @@ MakeGroupCommand::MakeGroupCommand(string option)  {
 						if (path == "") {	fastaFileNames[i] = inputDir + fastaFileNames[i];		}
 					}
 	
-					int ableToOpen;
 					ifstream in;
-					
-					ableToOpen = openInputFile(fastaFileNames[i], in);
+					int ableToOpen = openInputFile(fastaFileNames[i], in, "noerror");
+				
+					//if you can't open it, try default location
+					if (ableToOpen == 1) {
+						if (m->getDefaultPath() != "") { //default path is set
+							string tryPath = m->getDefaultPath() + getSimpleName(fastaFileNames[i]);
+							m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+							ableToOpen = openInputFile(tryPath, in, "noerror");
+							fastaFileNames[i] = tryPath;
+						}
+					}
 					in.close();
-
+					
 					if (ableToOpen == 1) { 
+						m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 						//erase from file list
 						fastaFileNames.erase(fastaFileNames.begin()+i);
 						i--;
 					}else{  filename += getRootName(getSimpleName(fastaFileNames[i]));  }
-					
 				}
 				
 				filename += "groups";