diff --git a/methylpy/__init__.py b/methylpy/__init__.py
index e398332..ac422f1 100755
--- a/methylpy/__init__.py
+++ b/methylpy/__init__.py
@@ -1 +1 @@
-__version__ = '1.3.2'
+__version__ = '1.3.4'
diff --git a/methylpy/call_mc_se.py b/methylpy/call_mc_se.py
index 0ee0cb2..1061d5f 100644
--- a/methylpy/call_mc_se.py
+++ b/methylpy/call_mc_se.py
@@ -629,6 +629,7 @@ def build_ref(input_files,
     else:
         subprocess.check_call(shlex.split(base_cmd + output + "_f.fasta " + output +"_f"))
         subprocess.check_call(shlex.split(base_cmd + output + "_r.fasta " + output+ "_r"))
+    subprocess.check_call(["rm",output + "_f.fasta",output + "_r.fasta"])
     return 0
     
 def convert_reads(inputf,output,buffer_line_number=100000):
diff --git a/methylpy/utilities.py b/methylpy/utilities.py
index 0756c70..4fc6b97 100644
--- a/methylpy/utilities.py
+++ b/methylpy/utilities.py
@@ -673,7 +673,7 @@ def index_allc_file(allc_file,reindex=False):
         # check index file completeness
         eof_count = 0
         line = False
-        with open(index_file,'r') as f:
+        with open(index_file,'r') as f:        
             for line in f:
                 if line == '#eof\n':
                     eof_count += 1
diff --git a/setup.py b/setup.py
index 0990b1b..8d44288 100644
--- a/setup.py
+++ b/setup.py
@@ -1,6 +1,6 @@
 from setuptools import setup
 
-methylpy_version = '1.3.2'
+methylpy_version = '1.3.4'
 
 setup(
     name='methylpy',