diff --git a/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
index 3eee8c22b..8336007e9 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
@@ -196,7 +196,7 @@ public abstract class MicroScheduler {
             ref = new IndexedFastaSequenceFile(refFile);
         }
         catch (FileNotFoundException ex) {
-            throw new RuntimeException("File not found opening fasta file; please do this check before MicroManaging", ex);
+            throw new StingException("I/O error while opening fasta file: " + ex.getMessage(), ex);
         }
         GenomeLoc.setupRefContigOrdering(ref);
         return ref;
diff --git a/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java b/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java
index 80643e06d..490826c86 100755
--- a/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java
+++ b/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java
@@ -31,7 +31,7 @@ public class FastaSequenceIndex implements Iterable {
      */
     public FastaSequenceIndex( File indexFile ) throws FileNotFoundException {
         if(!indexFile.exists())
-            throw new FileNotFoundException("Index file is missing");
+            throw new FileNotFoundException(String.format("Fasta index file is missing",indexFile.getAbsolutePath()));
 
         IoUtil.assertFileIsReadable(indexFile);
         parseIndexFile(indexFile);
diff --git a/java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java b/java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java
index 026a60cfc..d1a426e3f 100755
--- a/java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java
+++ b/java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java
@@ -90,6 +90,9 @@ public class IndexedFastaSequenceFile implements ReferenceSequenceFile {
      */
     private void loadIndex( File fastaFile ) throws FileNotFoundException {
         File indexFile = new File(fastaFile.getAbsolutePath() + ".fai");
+        if (!indexFile.exists())
+            throw new PicardException(String.format("Unable to load fasta index file %s.  "+
+                                                    "Please create it using 'samtools faidx'.",indexFile.getAbsolutePath()));
         index = new FastaSequenceIndex(indexFile);
         indexIterator = index.iterator();
     }