diff --git a/src/gtnet/sequence.py b/src/gtnet/sequence.py
index f3d15f1..5489486 100644
--- a/src/gtnet/sequence.py
+++ b/src/gtnet/sequence.py
@@ -34,6 +34,8 @@ def __init__(self, window, step, vocab=None, padval=None, min_seq_len=100, devic
         self.device = device
 
     def encode(self, seq):
+        if len(seq) < self.min_seq_len:
+            raise ValueError(f"Minimum sequence length is {self.min_seq_len} - got {len(seq)}")
         if seq.dtype == np.dtype('S1'):
             seq = seq.view(np.uint8)
         elif seq.dtype == np.dtype('U1'):
@@ -143,9 +145,14 @@ def readfiles(cls, encoder, fastas):
         for fa in fastas:
             logging.debug(f'loading {fa}')
             for seqid, values in cls.readfile(fa):
-                batches = encoder.encode(values)
-                val = (fa, seqid, len(values), batches)
-                yield val
+                if len(values) < encoder.min_seq_len:
+                    logging.warning((f"Skipping {seqid} from {fa} - length less than "
+                                    "minimum sequence length {encoder.min_seq}"))
+                    yield (fa, seqid, len(values), torch.zeros((0, 0, 0), dtype=torch.uint8))
+                else:
+                    batches = encoder.encode(values)
+                    val = (fa, seqid, len(values), batches)
+                    yield val
 
 
 class SerialLoader(Loader):