diff --git a/graphgen/bases/base_operator.py b/graphgen/bases/base_operator.py
index 30c71271..ad7c3a7c 100644
--- a/graphgen/bases/base_operator.py
+++ b/graphgen/bases/base_operator.py
@@ -92,8 +92,11 @@ def __call__(
                 is_first = True
                 for res in result:
                     yield pd.DataFrame([res])
-                    self.store([res], meta_update if is_first else {})
+                    self.store(
+                        [res], meta_update if is_first else {}, flush=False
+                    )
                     is_first = False
+                self.kv_storage.index_done_callback()
             else:
                 yield pd.DataFrame(result)
                 self.store(result, meta_update)
@@ -141,7 +144,7 @@ def split(self, batch: "pd.DataFrame") -> tuple["pd.DataFrame", "pd.DataFrame"]:
         recovered_chunks = [c for c in recovered_chunks if c is not None]
         return to_process, pd.DataFrame(recovered_chunks)
 
-    def store(self, results: list, meta_update: dict):
+    def store(self, results: list, meta_update: dict, flush: bool = True):
         results = convert_to_serializable(results)
         meta_update = convert_to_serializable(meta_update)
 
@@ -159,7 +162,8 @@ def store(self, results: list, meta_update: dict):
             for v in v_list:
                 inverse_meta[v] = k
         self.kv_storage.update({"_meta_inverse": inverse_meta})
-        self.kv_storage.index_done_callback()
+        if flush:
+            self.kv_storage.index_done_callback()
 
     @abstractmethod
     def process(self, batch: list) -> Tuple[Union[list, Iterable[dict]], dict]:
diff --git a/graphgen/storage/kv/rocksdb_storage.py b/graphgen/storage/kv/rocksdb_storage.py
index d1361169..9b373791 100644
--- a/graphgen/storage/kv/rocksdb_storage.py
+++ b/graphgen/storage/kv/rocksdb_storage.py
@@ -1,3 +1,4 @@
+import logging
 import os
 from dataclasses import dataclass
 from typing import Any, Dict, List, Set
@@ -8,6 +9,8 @@
 
 from graphgen.bases.base_storage import BaseKVStorage
 
+logger = logging.getLogger(__name__)
+
 
 @dataclass
 class RocksDBKVStorage(BaseKVStorage):
@@ -17,8 +20,10 @@ class RocksDBKVStorage(BaseKVStorage):
     def __post_init__(self):
         self._db_path = os.path.join(self.working_dir, f"{self.namespace}.db")
         self._db = Rdict(self._db_path)
-        print(
-            f"RocksDBKVStorage initialized for namespace '{self.namespace}' at '{self._db_path}'"
+        logger.debug(
+            "RocksDBKVStorage initialized for namespace '%s' at '%s'",
+            self.namespace,
+            self._db_path,
         )
 
     @property
@@ -30,7 +35,7 @@ def all_keys(self) -> List[str]:
 
     def index_done_callback(self):
         self._db.flush()
-        print(f"RocksDB flushed for {self.namespace}")
+        logger.debug("RocksDB flushed for %s", self.namespace)
 
     def get_by_id(self, id: str) -> Any:
         return self._db.get(id, None)