diff --git a/src/caosadvancedtools/loadFiles.py b/src/caosadvancedtools/loadFiles.py
index 56d50e4dd28df2098c6bc16b5300731948b076ac..f29bdd9e27c480d01313bc6c74553a5b6f3bebbf 100755
--- a/src/caosadvancedtools/loadFiles.py
+++ b/src/caosadvancedtools/loadFiles.py
@@ -375,9 +375,7 @@ exclude is given preference over include.
     logger.addHandler(logging.StreamHandler(stream=sys.stdout))
     logger.setLevel(logging.INFO)
 
-    con = db.get_connection()
-    con.timeout = float(args.timeout)
-    con._login()
+    db.configure_connection(timeout=float(args.timeout))
 
     loadpath(
         path=args.path,
diff --git a/src/caosadvancedtools/pandoc_header_tools.py b/src/caosadvancedtools/pandoc_header_tools.py
index fec27cdbb33cf963d01e40b61c04ae2613f5fe17..a0191e5a7880edb7aa378ad4f3f67f13fae28edb 100644
--- a/src/caosadvancedtools/pandoc_header_tools.py
+++ b/src/caosadvancedtools/pandoc_header_tools.py
@@ -107,12 +107,10 @@ it is not at the beginning, it must be preceded by a blank line.
         textlines = f.readlines()
 
     state = 0
-    found_0 = -1
     found_1 = -1
     found_2 = -1
     for i, line in enumerate(textlines):
         if len(line) == 1 and state in {-1, 0}:
-            found_0 = i
             state = 0
             continue
         if line.rstrip() == "---" and state == 0:
diff --git a/src/caosadvancedtools/suppressKnown.py b/src/caosadvancedtools/suppressKnown.py
index 1b31de7e9d8f1fdce35a135d558dd5ceea3bca2a..aada4ef64df6a496c4d1c30006cca23bd3e329c8 100644
--- a/src/caosadvancedtools/suppressKnown.py
+++ b/src/caosadvancedtools/suppressKnown.py
@@ -28,6 +28,7 @@ class SuppressKnown(logging.Filter):
     """
 
     def __init__(self, db_file=None):
+        super().__init__()
         if db_file:
             self.db_file = db_file
         else:
diff --git a/src/caosadvancedtools/utils.py b/src/caosadvancedtools/utils.py
index 43ecb3f2df276a4bb35de8d85f1c3f1994744b65..f64900c04e8f1d126a7299662a2b529aa9f027b8 100644
--- a/src/caosadvancedtools/utils.py
+++ b/src/caosadvancedtools/utils.py
@@ -27,7 +27,7 @@ import logging
 import os
 
 import linkahead as db
-from linkahead.exceptions import TransactionError
+from linkahead.exceptions import TransactionError, BadQueryError
 
 logger = logging.getLogger(__name__)
 
@@ -232,7 +232,7 @@ def find_records_that_reference_ids(referenced_ids, rt="", step_size=50):
                             [str(el) for el in subset]))
             exps = db.execute_query(q_string)
             record_ids.update([exp.id for exp in exps])
-        except Exception as e:
+        except (TransactionError, BadQueryError) as e:
             print(e)
 
         index += step_size