diff --git a/tools/rebuildEM/main.cpp b/tools/rebuildEM/main.cpp
index 2dc187fc5..3b82843e4 100644
--- a/tools/rebuildEM/main.cpp
+++ b/tools/rebuildEM/main.cpp
@@ -89,8 +89,7 @@ int main(int argc, char** argv)
     std::cout << "The launch of mcsRebuildEM tool must be sanctioned by MariaDB support. "
               << std::endl;
     std::cout << "Requirement: all DBRoots must be on this node. " << std::endl;
-    std::cout << "Note: that the launch can break the cluster." << std::endl;
-    std::cout << "Do you want to continue Y/N? " << std::endl;
+    std::cout << "Do you want to continue Y/N? ";
     std::string confirmation;
     cin >> confirmation;
     if (confirmation.size() == 0)
@@ -124,6 +123,7 @@ int main(int argc, char** argv)
         std::cout << "If `BRM_saves_em` "
                      "exists extent map will be restored from it. "
                   << std::endl;
+        std::cout << "Exiting. " << std::endl;
         return 0;
     }
 
@@ -131,6 +131,8 @@ int main(int argc, char** argv)
     auto rc = emReBuilder.initializeSystemExtents();
     if (rc == -1)
     {
+        std::cerr << "Cannot initialize system extents from binary blob." << std::endl;
+        std::cerr << "Exiting. " << std::endl;
         return 1;
     }
 
@@ -151,5 +153,8 @@ int main(int argc, char** argv)
         emReBuilder.clear();
     }
 
+    // Save restored extent map.
+    emReBuilder.getEM().save(BRMSavesEM);
+    std::cout << "Completed." << std::endl;
     return 0;
 }
diff --git a/tools/rebuildEM/rebuildEM.cpp b/tools/rebuildEM/rebuildEM.cpp
index cb0d20b40..d74e7a942 100644
--- a/tools/rebuildEM/rebuildEM.cpp
+++ b/tools/rebuildEM/rebuildEM.cpp
@@ -65,9 +65,7 @@ int32_t EMReBuilder::collectExtent(const std::string& fullFileName)
     auto rc = WriteEngine::Convertor::fileName2Oid(fullFileName, oid,
                                                    partition, segment);
     if (rc != 0)
-    {
         return rc;
-    }
 
     // Open the given file.
     std::unique_ptr<IDBDataFile> dbFile(IDBDataFile::open(
@@ -97,12 +95,11 @@ int32_t EMReBuilder::collectExtent(const std::string& fullFileName)
         // have a header block, so header verification fails in this case,
         // currently we skip it, because we cannot deduce needed data to create
         // a column extent from the blob file.
-        if (doVerbose())
+        // Skip fileID from system catalog.
+        if (doVerbose() && oid > 3000)
         {
-            std::cerr
-                << "Cannot read file header from the file " << fullFileName
-                << ", probably this file was created without compression. "
-                << std::endl;
+            std::cerr << "Cannot read file header from the file " << fullFileName
+                      << ", probably this file was created without compression. " << std::endl;
         }
         return rc;
     }
@@ -138,9 +135,8 @@ int32_t EMReBuilder::collectExtent(const std::string& fullFileName)
     if (colDataType == execplan::CalpontSystemCatalog::UNDEFINED)
     {
         if (doVerbose())
-        {
             std::cout << "File header has invalid data. " << std::endl;
-        }
+
         return -1;
     }
 
@@ -158,14 +154,10 @@ int32_t EMReBuilder::collectExtent(const std::string& fullFileName)
     rc = searchHWMInSegmentFile(oid, getDBRoot(), partition, segment, colDataType, colWidth,
                                 blockCount, isDict, compressionType, hwm);
     if (rc != 0)
-    {
         return rc;
-    }
 
     if (doVerbose())
-    {
         std::cout << "HWM is: " << hwm << std::endl;
-    }
 
     const uint32_t extentMaxBlockCount = getEM().getExtentRows() * colWidth / BLOCK_SIZE;
     // We found multiple extents per one segment file.
@@ -198,9 +190,7 @@ int32_t EMReBuilder::collectExtent(const std::string& fullFileName)
         extentMap.push_back(fileId);
 
         if (doVerbose())
-        {
             std::cout << "FileId is collected " << fileId << std::endl;
-        }
     }
 
     return 0;