diff --git a/mhcflurry/train_pan_allele_models_command.py b/mhcflurry/train_pan_allele_models_command.py
index 2334850b11090706e02f4c20369531ad5154430c..a608f8aae79b64fe8fb5fd88a88677c90ab4f683 100644
--- a/mhcflurry/train_pan_allele_models_command.py
+++ b/mhcflurry/train_pan_allele_models_command.py
@@ -309,7 +309,7 @@ def initialize_training(args):
     pprint.pprint(hyperparameters_lst)
 
     allele_sequences = pandas.read_csv(
-        args.allele_sequences, index_col=0).sequence
+        args.allele_sequences, index_col=0).iloc[:,0]
 
     df = pandas.read_csv(args.data)
     print("Loaded training data: %s" % (str(df.shape)))