diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
index ed5a4492e9caa4ad9e77f4ffd431c1a70c6b0b57..bcdabfaeb1f95ed3bade6df058b3b9ae2b291f96 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
@@ -121,7 +121,6 @@ object Reference {
    */
   def requireFai(fastaFile: File): Unit = {
     val fai = new File(fastaFile.getAbsolutePath + ".fai")
-    require(fai.exists(), "Reference is missing a fai file")
     if (fai.exists()) {
       if (!IndexedFastaSequenceFile.canCreateIndexedFastaReader(fastaFile))
         Logging.addError(s"Index of reference cannot be loaded, reference: $fastaFile")