diff --git a/src/main/java/htsjdk/samtools/cram/encoding/reader/DataReaderFactory.java b/src/main/java/htsjdk/samtools/cram/encoding/reader/DataReaderFactory.java
index 4e5c4ec02..253ab1521 100644
--- a/src/main/java/htsjdk/samtools/cram/encoding/reader/DataReaderFactory.java
+++ b/src/main/java/htsjdk/samtools/cram/encoding/reader/DataReaderFactory.java
@@ -56,9 +56,7 @@ public AbstractReader buildReader(final AbstractReader reader,
                 final DataSeries dataSeries = field.getAnnotation(DataSeries.class);
                 final EncodingKey key = dataSeries.key();
                 final DataSeriesType type = dataSeries.type();
-                if (header.encodingMap.get(key) == null) {
-                    log.debug("Encoding not found for key: " + key);
-                } else {
+                if (header.encodingMap.get(key) != null) {
                     try {
                         field.set(reader,
                                 createReader(type, header.encodingMap.get(key), bitInputStream, inputMap));
diff --git a/src/main/java/htsjdk/samtools/cram/structure/CompressionHeader.java b/src/main/java/htsjdk/samtools/cram/structure/CompressionHeader.java
index 323b3f690..2278bf17e 100644
--- a/src/main/java/htsjdk/samtools/cram/structure/CompressionHeader.java
+++ b/src/main/java/htsjdk/samtools/cram/structure/CompressionHeader.java
@@ -17,6 +17,7 @@
  */
 package htsjdk.samtools.cram.structure;
 
+import htsjdk.samtools.cram.CRAMException;
 import htsjdk.samtools.cram.encoding.ExternalCompressor;
 import htsjdk.samtools.cram.encoding.NullEncoding;
 import htsjdk.samtools.cram.io.ITF8;
@@ -170,8 +171,7 @@ else if (TD_tagIdsDictionary.equals(key)) {
                 final String key = new String(new byte[]{buffer.get(), buffer.get()});
                 final EncodingKey encodingKey = EncodingKey.byFirstTwoChars(key);
                 if (encodingKey == null) {
-                    log.debug("Unknown encoding key: " + key);
-                    continue;
+                    throw new CRAMException("Unknown encoding key: " + key);
                 }
 
                 final EncodingID id = EncodingID.values()[buffer.get()];