diff --git a/src/main/java/picard/fingerprint/CheckFingerprint.java b/src/main/java/picard/fingerprint/CheckFingerprint.java
index 9a8e926fa..8bc4fbbcb 100644
--- a/src/main/java/picard/fingerprint/CheckFingerprint.java
+++ b/src/main/java/picard/fingerprint/CheckFingerprint.java
@@ -155,7 +155,7 @@ protected int doWork() {
             SequenceUtil.assertSequenceDictionariesEqual(SAMSequenceDictionaryExtractor.extractDictionary(INPUT), checker.getHeader().getSequenceDictionary(), true);
 
             // Verify that there's only one sample in the SAM/BAM.
-            final SamReader in = SamReaderFactory.makeDefault().open(INPUT);
+            final SamReader in = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT);
             for (final SAMReadGroupRecord rec : in.getFileHeader().getReadGroups()) {
                 if (observedSampleAlias == null) {
                     observedSampleAlias = rec.getSample();