diff --git a/ppanggolin/nem/partition.py b/ppanggolin/nem/partition.py
index 980480dc..952ab583 100644
--- a/ppanggolin/nem/partition.py
+++ b/ppanggolin/nem/partition.py
@@ -166,26 +166,14 @@ def run_partitioning(nem_dir_path: Path, nb_org: int, beta: float = 2.5, free_di
                     else:
                         partitions_list[i] = parti[positions_max_prob.pop()]
     except OSError:
-        logging.getLogger("PPanGGOLiN").debug(
-            "partitioning did not work (the number of genomes used is probably too low), "
-            "see logs here to obtain more details " + nem_dir_path.as_posix() + "/nem_file_" +
-            str(kval) + ".log")
+        logging.getLogger("PPanGGOLiN").warning("Partitioning did not work (the number of genomes used is probably too low), "
+            f"see logs here to obtain more details {nem_dir_path.as_posix()}")
         return {}, None, None  # return empty objects
+
     except ValueError:
         # return the default partitions_list which correspond to undefined
         pass
 
-    if not keep_files and no_nem is False:
-        os.remove(nem_dir_path / f"nem_file_{str(kval)}.uf")
-        os.remove(nem_dir_path / f"nem_file_{str(kval)}.mf")
-        os.remove(nem_dir_path / f"nem_file_{str(kval)}.log")
-        os.remove(nem_dir_path / f"nem_file_{str(kval)}.stderr")
-        os.remove(nem_dir_path / f"nem_file_init_{str(kval)}.m")
-        os.remove(nem_dir_path / "nem_file.index")
-        os.remove(nem_dir_path / "nem_file.dat")
-        os.remove(nem_dir_path / "nem_file.nei")
-        os.remove(nem_dir_path / "nem_file.str")
-
     if just_log_likelihood:
         return kval, log_likelihood, entropy
     else:
@@ -469,8 +457,15 @@ def partition(pangenome: Pangenome, output: Path = None, beta: float = 2.5, sm_d
     check_pangenome_former_partition(pangenome, force)
     check_pangenome_info(pangenome, need_annotations=True, need_families=True, need_graph=True, disable_bar=disable_bar)
     organisms = set(pangenome.organisms)
-    tmp_dir = tempfile.TemporaryDirectory(dir=tmpdir)
-    tmp_path = Path(tmp_dir.name)
+
+    if keep_tmp_files:
+        # Create a temporary directory without auto-cleanup
+        tmp_dir = tempfile.mkdtemp(dir=tmpdir)
+        tmp_path = Path(tmp_dir)
+    else:
+        # Create a temporary directory with auto-cleanup
+        tmp_dir = tempfile.TemporaryDirectory(dir=tmpdir)
+        tmp_path = Path(tmp_dir.name)
 
     if len(organisms) <= 10:
         logging.getLogger("PPanGGOLiN").warning(f"The number of selected genomes is too low ({len(organisms)} "