diff --git a/modisco/metaclusterers.py b/modisco/metaclusterers.py
index 59ddafd..4ecd7c3 100644
--- a/modisco/metaclusterers.py
+++ b/modisco/metaclusterers.py
@@ -105,7 +105,8 @@ def fit(self, seqlets):
                              self.get_vector_from_seqlet(x) 
                              for x in seqlets]))
         self._fit(attribute_vectors)
-        self.fit_called = True 
+        self.fit_called = True
+        return self
 
     def _fit(self, attribute_vectors):
         raise NotImplementedError()
@@ -159,6 +160,11 @@ def weak_vector_to_pattern(self, vector):
             assert False
         return to_return
     
+    def get_all_possible_compatible_patterns(self, pattern):
+        all_possible_patterns = list(
+            itertools.product(*[(x,0) for x in pattern]))
+        return all_possible_patterns
+    
     def check_pattern_compatibility(self, pattern_to_check, reference_pattern):
         return all([(pattern_elem==reference_elem or reference_elem==0)
                     for pattern_elem, reference_elem
@@ -287,17 +293,15 @@ def save_hdf5(self, grp):
     
     def _fit(self, attribute_vectors):
 
-        all_possible_activity_patterns =\
-            list(itertools.product(*[(1,-1,0) for x
-                 in range(attribute_vectors.shape[1])]))
+        all_possible_activity_patterns = set()
 
         activity_pattern_to_attribute_vectors = defaultdict(list)        
         for vector in attribute_vectors:
             vector_activity_pattern = self.vector_to_pattern(vector)
             compatible_activity_patterns =\
-                self.get_compatible_patterns(
-                     vector_activity_pattern, all_possible_activity_patterns)
+                self.get_all_possible_compatible_patterns(vector_activity_pattern)
             for compatible_activity_pattern in compatible_activity_patterns:
+                all_possible_activity_patterns.add(compatible_activity_pattern)
                 activity_pattern_to_attribute_vectors[
                     self.pattern_to_str(
                          compatible_activity_pattern)].append(vector)
diff --git a/modisco/tfmodisco_workflow/workflow.py b/modisco/tfmodisco_workflow/workflow.py
index a42e3b8..02d906a 100644
--- a/modisco/tfmodisco_workflow/workflow.py
+++ b/modisco/tfmodisco_workflow/workflow.py
@@ -157,7 +157,8 @@ def __init__(self,
                  max_passing_windows_frac=0.2,
                  separate_pos_neg_thresholds=False,
                  verbose=True,
-                 min_seqlets_per_task=None):
+                 min_seqlets_per_task=None,
+                 max_seqlets_during_metacluster_fit=np.inf):
 
         if (min_seqlets_per_task is not None):
             raise DeprecationWarning(
@@ -180,6 +181,7 @@ def __init__(self,
         self.max_passing_windows_frac = max_passing_windows_frac
         self.separate_pos_neg_thresholds = separate_pos_neg_thresholds
         self.verbose = verbose
+        self.max_seqlets_during_metacluster_fit = max_seqlets_during_metacluster_fit
 
         self.build()
 
@@ -248,11 +250,12 @@ def __call__(self, task_names, contrib_scores,
                   +" Consider dropping target_seqlet_fdr") 
 
         
-        if int(self.min_metacluster_size_frac * len(seqlets)) > self.min_metacluster_size:
-            print("min_metacluster_size_frac * len(seqlets) = {0} is more than min_metacluster_size={1}.".\
-                  format(int(self.min_metacluster_size_frac * len(seqlets)), self.min_metacluster_size))
+        if int(self.min_metacluster_size_frac
+               * min(len(seqlets),self.max_seqlets_during_metacluster_fit)) > self.min_metacluster_size:
+            print("min_metacluster_size_frac * min(len(seqlets),self.max_seqlets_during_metacluster_fit) = {0} is more than min_metacluster_size={1}.".\
+                  format(int(self.min_metacluster_size_frac * min(len(seqlets),self.max_seqlets_during_metacluster_fit)), self.min_metacluster_size))
             print("Using it as a new min_metacluster_size")
-            self.min_metacluster_size = int(self.min_metacluster_size_frac * len(seqlets))
+            self.min_metacluster_size = int(self.min_metacluster_size_frac * min(len(seqlets),self.max_seqlets_during_metacluster_fit))
 
 
         if (self.weak_threshold_for_counting_sign is None):
@@ -288,7 +291,13 @@ def __call__(self, task_names, contrib_scores,
                                 weak_threshold_for_counting_sign=
                                     weak_threshold_for_counting_sign)
 
-        metaclustering_results = metaclusterer.fit_transform(seqlets)
+        if (len(seqlets) > self.max_seqlets_during_metacluster_fit):
+            indices = np.random.RandomState(1234).choice(
+                a=len(seqlets), size=self.max_seqlets_during_metacluster_fit, replace=False)
+            seqlets_to_metacluster = [seqlets[x] for x in indices]
+        else:
+            seqlets_to_metacluster = seqlets
+        metaclustering_results = metaclusterer.fit(seqlets_to_metacluster).transform(seqlets)
         metacluster_indices = np.array(
             metaclustering_results.metacluster_indices)
         metacluster_idx_to_activity_pattern =\
diff --git a/setup.py b/setup.py
index 9b69175..a035367 100644
--- a/setup.py
+++ b/setup.py
@@ -6,7 +6,7 @@
           description='TF MOtif Discovery from Importance SCOres',
           long_description="""Algorithm for discovering consolidated patterns from base-pair-level importance scores""",
           url='https://github.com/kundajelab/tfmodisco',
-          version='0.5.1.2',
+          version='0.5.1.3',
           packages=find_packages(),
           package_data={
                 '': ['cluster/phenograph/louvain/*convert*', 'cluster/phenograph/louvain/*community*', 'cluster/phenograph/louvain/*hierarchy*']