diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
index f4ce5071c..5122b691c 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
@@ -161,6 +161,8 @@ public class SAMDataSource implements SimpleDataSource {
      * @return an iterator for that region
      */
     private StingSAMIterator seekLocus( GenomeLoc location ) throws SimpleDataSourceLoadException {
+        if( getHeader().getSequenceDictionary().getSequences().size() == 0 )
+            throw new StingException("Unable to seek to the given locus; reads data source has no alignment information.");
         return createIterator( new MappedStreamSegment(location) );
     }