diff --git a/hybpiper/paralog_retriever.py b/hybpiper/paralog_retriever.py
index 17ae18c..85eaad8 100755
--- a/hybpiper/paralog_retriever.py
+++ b/hybpiper/paralog_retriever.py
@@ -569,7 +569,7 @@ def main(args):
         else:
             try:
                 with open(f'{sampledir_parent}/{chimera_check_performed_file}', 'r') as chimera_check_handle:
-                    chimera_check_bool = chimera_check_handle.read()
+                    chimera_check_bool = chimera_check_handle.read().rstrip()
             except FileNotFoundError:
                 logger.error(chimera_file_fill)
                 sys.exit(1)
diff --git a/hybpiper/retrieve_sequences.py b/hybpiper/retrieve_sequences.py
index dc40f8d..f2f5c72 100644
--- a/hybpiper/retrieve_sequences.py
+++ b/hybpiper/retrieve_sequences.py
@@ -298,7 +298,7 @@ def recover_sequences_from_all_samples(seq_dir,
                 else:
                     try:
                         with open(f'{sampledir_parent}/{chimera_check_performed_file}', 'r') as chimera_check_handle:
-                            chimera_check_bool = chimera_check_handle.read()
+                            chimera_check_bool = chimera_check_handle.read().rstrip()
                     except FileNotFoundError:
                         logger.error(chimera_file_fill)
                         sys.exit(1)
@@ -477,7 +477,7 @@ def recover_sequences_from_one_sample(seq_dir,
     else:
         try:
             with open(f'{sampledir_parent}/{chimera_check_performed_file}', 'r') as chimera_check_handle:
-                chimera_check_bool = chimera_check_handle.read()
+                chimera_check_bool = chimera_check_handle.read().rstrip()
         except FileNotFoundError:
             logger.error(chimera_file_fill)
             sys.exit(1)