diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py
index 65094eb41dc..b9ab50733f3 100644
--- a/lib/galaxy/datatypes/sequence.py
+++ b/lib/galaxy/datatypes/sequence.py
@@ -54,23 +54,16 @@ class Maf( Alignment ):
         """
         species = []
         try:
-            maf_reader = bx.align.maf.Reader( open(dataset.file_name) )
-            for i, m in enumerate( maf_reader ):
-                l = m.components
-                for c in l:
+            for i, m in enumerate( bx.align.maf.Reader( open(dataset.file_name) ) ):
+                for c in m.components:
                     spec,chrom = bx.align.maf.src_split( c.src )
-                    if not spec or not chrom:
-                        spec = chrom = c.src
-                    if spec not in species:
-                        species.append(spec)
-                #only check first million blocks for species
-                if i > 1000000:
-                    break
-        except:
-            pass
+                    if not spec or not chrom: spec = chrom = c.src
+                    if spec not in species: species.append(spec)
+                #only check first 100,000 blocks for species
+                if i > 100000: break
+        except: pass
         dataset.metadata.species = species
 
-
 class Axt( Alignment ):
     """Class describing an axt alignment"""
 
diff --git a/scripts/update_metadata.py b/scripts/update_metadata.py
index 2ffab49b1ae..426b9454f59 100644
--- a/scripts/update_metadata.py
+++ b/scripts/update_metadata.py
@@ -20,35 +20,46 @@ def main():
     for key, value in conf_parser.items("app:main"): configuration[key] = value
     app = galaxy.app.UniverseApplication( global_conf = ini_file, **configuration )
     
-    # Step through Database, turning metadata bunches into dictionaries.
-    print "Changing metadata bunches to dictionaries."
-    for row in app.model.Dataset.table.select().execute():
-        if isinstance (row.metadata, Bunch):
-            print row.id
-            app.model.Dataset.table.update(app.model.Dataset.table.c.id == row.id).execute( _metadata = row.metadata.__dict__ )
+    #Step through Database, turning metadata bunches into dictionaries.
+    #print "Changing metadata bunches to dictionaries."
+    #for row in app.model.Dataset.table.select().execute():
+    #    if isinstance (row.metadata, Bunch):
+    #        print row.id
+    #        app.model.Dataset.table.update(app.model.Dataset.table.c.id == row.id).execute( _metadata = row.metadata.__dict__ )
     
-    print "Rewriting all metadata to database, setting metadata dbkey, to ensure JSONified storage."
     #Make sure all metadata is jsonified
-    for row in app.model.Dataset.table.select().execute():
-        print row.id
-        data = app.model.Dataset.get(row.id)
-        dbkey = data.old_dbkey
-        if not dbkey or data.metadata.dbkey not in ["?", ["?"], None, []]:
-            dbkey = data.metadata.dbkey
-        if not dbkey: dbkey = "?"
-        #change dbkey then flush, then change to real value and flush, ensures that metadata is rewritten to database
-        data.dbkey="~"
-        data.flush()
-        data.dbkey=dbkey
-        data.flush()
+    #print "Rewriting all metadata to database, setting metadata dbkey, to ensure JSONified storage."
+    #for row in app.model.Dataset.table.select().execute():
+    #    print row.id
+    #    data = app.model.Dataset.get(row.id)
+    #    dbkey = data.old_dbkey
+    #    if not dbkey or data.metadata.dbkey not in ["?", ["?"], None, []]:
+    #        dbkey = data.metadata.dbkey
+    #    if not dbkey: dbkey = "?"
+    #    #change dbkey then flush, then change to real value and flush, ensures that metadata is rewritten to database
+    #    data.dbkey="~"
+    #    data.flush()
+    #    data.dbkey=dbkey
+    #    data.flush()
+    
     
-    print "Seeking out tabular based files and setting number of columns."
     #Search out tabular datatypes and make sure that number of columns is set.
-    for row in app.model.Dataset.table.select().execute():
+    #print "Seeking out tabular based files and setting number of columns."
+    #for row in app.model.Dataset.table.select().execute():
+    #    data = app.model.Dataset.get(row.id)
+    #    if issubclass(type(data.datatype), type(app.datatypes_registry.get_datatype_by_extension('tabular'))):
+    #        print row.id
+    #        galaxy.datatypes.tabular.Tabular().set_meta( data ) #Call tabular set metadata method for all Classes, this will set number of columns.
+    #        data.flush()
+            
+    #Search out maf datatypes and make sure that available species is set.
+    print "Seeking out maf files and setting available species."
+    for row in app.model.Dataset.table.select(app.model.Dataset.table.c.extension == 'maf').execute():
+        print row.id
+        sys.stdout.flush()
         data = app.model.Dataset.get(row.id)
-        if issubclass(type(data.datatype), type(app.datatypes_registry.get_datatype_by_extension('tabular'))):
-            print row.id
-            galaxy.datatypes.tabular.Tabular().set_meta( data ) #Call tabular set metadata method for all Classes, this will set number of columns.
+        if data.missing_meta:
+            data.set_meta() #Call maf set metadata method, setting available species
             data.flush()
     
     app.shutdown()