Added a better error handling on a missing reference.

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala

@@ -94,12 +94,12 @@ trait Reference extends Configurable {
     )
   }
 
-  //TODO: this become obsolete when index get autogenerated
+  //TODO: this become obsolete when index get auto generated
 
   /** Check fasta file if file exist and index file are there */
   def checkFasta(file: File): Unit = {
     if (!Reference.checked.contains(file)) {
-      require(file.exists(), "Reference not found: " + file)
+      if (!file.exists()) BiopetQScript.addError(s"Reference not found: $file, species: $referenceSpecies, name: $referenceName, configValue: " + config("reference_fasta"))
 
       if (dictRequired) Reference.requireDict(file)
       if (faiRequired) Reference.requireFai(file)