diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/MongoDBAdaptorFactory.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/MongoDBAdaptorFactory.java
index 019f2adb35..8bbec6ee7c 100644
--- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/MongoDBAdaptorFactory.java
+++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/MongoDBAdaptorFactory.java
@@ -17,7 +17,6 @@
 package org.opencb.opencga.catalog.db.mongodb;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.JsonMappingException;
 import org.apache.commons.lang3.StringUtils;
 import org.opencb.commons.datastore.core.DataStoreServerAddress;
 import org.opencb.commons.datastore.core.Query;
@@ -46,12 +45,16 @@
 import org.slf4j.LoggerFactory;
 
 import java.util.*;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
 
 /**
  * Created by pfurio on 08/01/16.
  */
 public class MongoDBAdaptorFactory implements DBAdaptorFactory {
 
+    private static final ExecutorService FUTURE_EXECUTOR = Executors.newSingleThreadExecutor();
+
     private final IOManagerFactory ioManagerFactory;
     private final MongoDataStoreManager mongoManager;
     private final MongoDBConfiguration mongoDbConfiguration;
@@ -285,17 +288,21 @@ public OpenCGAResult<Organization> createOrganization(Organization organization,
                 String orgSummaryString = JacksonUtils.getDefaultObjectMapper().writeValueAsString(organizationSummary);
                 Map<String, Object> value = JacksonUtils.getDefaultObjectMapper().readerFor(Map.class).readValue(orgSummaryString);
                 noteCreateParams.setValue(value);
-            } catch (JsonMappingException e) {
-                throw new RuntimeException(e);
             } catch (JsonProcessingException e) {
                 throw new RuntimeException(e);
             }
             Note note = noteCreateParams.toNote(Note.Scope.ORGANIZATION, userId);
             NoteManager.validateNewNote(note, userId);
 
-            // Create new database and indexes
-            organizationDBAdaptorFactory.createAllCollections();
-            organizationDBAdaptorFactory.createIndexes();
+            // Create new database and indexes in a non-blocking future transaction (~10 seconds)
+            FUTURE_EXECUTOR.submit(() -> {
+                try {
+                    organizationDBAdaptorFactory.createAllCollections();
+                    organizationDBAdaptorFactory.createIndexes();
+                } catch (Exception e) {
+                    logger.error("Could not create collections/indexes for Organization {}: {}", organization.getId(), e.getMessage(), e);
+                }
+            });
 
             // Create organization
             OpenCGAResult<Organization> result = organizationDBAdaptorFactory.getCatalogOrganizationDBAdaptor()
diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/OrganizationMongoDBAdaptorFactory.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/OrganizationMongoDBAdaptorFactory.java
index 71741f8ca0..2f9a482ded 100644
--- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/OrganizationMongoDBAdaptorFactory.java
+++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/OrganizationMongoDBAdaptorFactory.java
@@ -304,7 +304,8 @@ public void initialiseMetaCollection(Admin admin) throws CatalogException {
     }
 
     public void createAllCollections() throws CatalogDBException {
-        if (!mongoDataStore.getCollectionNames().isEmpty()) {
+        if (!mongoDataStore.getCollectionNames().isEmpty()
+                && mongoDataStore.getCollectionNames().containsAll(OrganizationMongoDBAdaptorFactory.COLLECTIONS_LIST)) {
             throw new CatalogDBException("Database " + mongoDataStore.getDatabaseName() + " already exists with the following "
                     + "collections: " + StringUtils.join(mongoDataStore.getCollectionNames()) + ".\nPlease, remove the database or"
                     + " choose a different one.");
diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/rest/OpenCGAWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/rest/OpenCGAWSServer.java
index 44e4092478..a57cadad46 100644
--- a/opencga-server/src/main/java/org/opencb/opencga/server/rest/OpenCGAWSServer.java
+++ b/opencga-server/src/main/java/org/opencb/opencga/server/rest/OpenCGAWSServer.java
@@ -65,8 +65,8 @@
 
 import javax.servlet.ServletContext;
 import javax.servlet.http.HttpServletRequest;
-import javax.ws.rs.QueryParam;
 import javax.ws.rs.*;
+import javax.ws.rs.QueryParam;
 import javax.ws.rs.core.*;
 import java.io.File;
 import java.io.FileInputStream;
@@ -77,6 +77,7 @@
 import java.nio.file.Paths;
 import java.util.*;
 import java.util.concurrent.Callable;
+import java.util.concurrent.Executors;
 import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.stream.Collectors;
 
@@ -269,6 +270,37 @@ static void init(String opencgaHomeStr) {
         logger.info("| - Version {}", GitRepositoryState.getInstance().getBuildVersion());
         logger.info("| - Git version: {} {}", GitRepositoryState.getInstance().getBranch(), GitRepositoryState.getInstance().getCommitId());
         logger.info("========================================================================\n");
+
+        logMigrationSummary();
+    }
+
+    private static void logMigrationSummary() {
+        Executors.newSingleThreadExecutor().submit(() -> {
+            try {
+                Map<String, MigrationSummary> migrationSummaryMap = catalogManager.getMigrationManager().getMigrationSummary();
+                logger.info("========================================================================");
+                logger.info("| Migration summary:");
+                boolean pendingMigrations = false;
+                for (Map.Entry<String, MigrationSummary> entry : migrationSummaryMap.entrySet()) {
+                    if (entry.getValue().getMigrationsToBeApplied() > 0) {
+                        pendingMigrations = true;
+                        logger.info("|  * Pending migrations for organization {}: {}", entry.getKey(),
+                                entry.getValue().getMigrationsToBeApplied());
+                        for (Map.Entry<MigrationRun.MigrationStatus, Long> entry2 : entry.getValue().getStatusCount().entrySet()) {
+                            if (entry2.getKey().toBeApplied() && entry2.getValue() > 0) {
+                                logger.info("|  *     {}: {}", entry2.getKey(), entry2.getValue());
+                            }
+                        }
+                    }
+                }
+                if (!pendingMigrations) {
+                    logger.info("|  All organizations are up to date. No pending migrations found.");
+                }
+                logger.info("========================================================================");
+            } catch (CatalogException e) {
+                logger.error("Error retrieving migration summary", e);
+            }
+        });
     }
 
     /**
@@ -302,19 +334,6 @@ private static void initOpenCGAObjects() {
             variantManager = new VariantStorageManager(catalogManager, storageEngineFactory);
             healthCheckMonitor = new OpenCGAHealthCheckMonitor(configuration, catalogManager, storageEngineFactory, variantManager);
             healthCheckMonitor.asyncUpdate();
-
-            Map<String, MigrationSummary> migrationSummaryMap = catalogManager.getMigrationManager().getMigrationSummary();
-            for (Map.Entry<String, MigrationSummary> entry : migrationSummaryMap.entrySet()) {
-                if (entry.getValue().getMigrationsToBeApplied() > 0) {
-                    logger.info("|  * Pending migrations for organization {}: {}", entry.getKey(),
-                            entry.getValue().getMigrationsToBeApplied());
-                    for (Map.Entry<MigrationRun.MigrationStatus, Long> entry2 : entry.getValue().getStatusCount().entrySet()) {
-                        if (entry2.getKey().toBeApplied() && entry2.getValue() > 0) {
-                            logger.info("|  *     {}: {}", entry2.getKey(), entry2.getValue());
-                        }
-                    }
-                }
-            }
         } catch (Exception e) {
             errorMessage = e.getMessage();
 //            e.printStackTrace();