diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
index 85dc6525595f3920d1e538e124d394317072f390..5567dd2296f9c9819d610bb18558668c878f8a14 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -667,8 +667,7 @@ class HHblits:
         job = subprocess.Popen(cs_cmd, shell=True, cwd=self.working_dir,
                                stdout=subprocess.PIPE, stderr=subprocess.PIPE)
         sout, _ = job.communicate()
-        sout = sout.decode()
-        if 'Wrote abstract state sequence to' in sout:
+        if b'Wrote abstract state sequence to' in sout:
             return cs_file
 
         ost.LogWarning('Creating column state sequence file (%s) failed' % \