diff --git a/src/obitools/ecopcr/sequence.py b/src/obitools/ecopcr/sequence.py
index 89e1a38..e1a5627 100644
--- a/src/obitools/ecopcr/sequence.py
+++ b/src/obitools/ecopcr/sequence.py
@@ -64,12 +64,14 @@ class EcoPCRDBSequenceIterator(EcoPCRDBFile):
 class EcoPCRDBSequenceWriter(object):
     
     def __init__(self,options,fileidx=None,ftid=None,type=None,definition=None,append=False):
-
+        from obitools.options import currentInputFileName
+        self.currentInputFileName=currentInputFileName
         # Take care of the taxonomy associated to the database
+        self._currentfile=None
         
         self._taxonomy= loadTaxonomyDatabase(options)
         dbname = options.ecopcroutput
-
+        
         if (self._taxonomy is not None
             and (not hasattr(options,'ecodb') or options.ecodb!=dbname)):
             print >> sys.stderr,"Writing the taxonomy file...",
@@ -82,23 +84,25 @@ class EcoPCRDBSequenceWriter(object):
             fileidx = max(list(int(p.search(i).group(1)) 
                                for i in glob('%s_[0-9][0-9][0-9].sdx' % dbname))+[0]
                           ) +1
+                          
+        self._fileidx=fileidx
+        self._dbname=dbname
+        
         
         self._filename="%s_%03d.sdx" % (dbname,fileidx)
         if append:
-            mode ='r+b'
             f = universalOpen(self._filename)
             (recordCount,) = struct.unpack('> I',f.read(4))
             self._sequenceCount=recordCount
+            self._sequenceFileCount=recordCount
             del f
-            self._file = open(self._filename,mode)
-            self._file.seek(0,0)
-            self._file.write(struct.pack('> I',0))
+            self.open('r+b')
             self._file.seek(0,2)
+
         else:
             self._sequenceCount=0
-            mode = 'wb'
-            self._file = open(self._filename,mode)
-            self._file.write(struct.pack('> I',self._sequenceCount))
+            self._sequenceFileCount=0
+            self.open("wb")
                 
         if type is not None:
             assert ftid is not None,"You must specify an id attribute for features"
@@ -141,7 +145,28 @@ class EcoPCRDBSequenceWriter(object):
         return packed
 
         
+    def close(self):
+        self._file.seek(0,0)
+        self._file.write(struct.pack('> I',self._sequenceFileCount))
+        self._file.close()
+            
+    def open(self,mode):
+            self._filename="%s_%03d.sdx" % (self._dbname,self._fileidx)
+            self._file=open(self._filename,mode)
+            self._sequenceFileCount=0
+            self._file.write(struct.pack('> I',self._sequenceFileCount))
+        
     def put(self,sequence):
+        if self._currentfile is None:
+            self._currentfile=self.currentInputFileName()
+        if self.currentInputFileName() != self._currentfile:
+            self._currentfile=self.currentInputFileName()
+
+            self.close()
+
+            self._fileidx+=1
+            self.open('wb')
+            
         if self._taxonomy is not None:
             if 'taxid' not in sequence and hasattr(sequence, 'extractTaxon'):
                 sequence.extractTaxon()
@@ -149,11 +174,10 @@ class EcoPCRDBSequenceWriter(object):
         if self._annotation is not None:
             self._annotation.put(sequence, self._sequenceCount)
         self._sequenceCount+=1
+        self._sequenceFileCount+=1
         
     def __del__(self):
-        self._file.seek(0,0)
-        self._file.write(struct.pack('> I',self._sequenceCount))
-        self._file.close()
+        self.close()
             
         
     
diff --git a/src/obitools/options/_options.pyx b/src/obitools/options/_options.pyx
index f9b8250..c972215 100644
--- a/src/obitools/options/_options.pyx
+++ b/src/obitools/options/_options.pyx
@@ -93,7 +93,7 @@ def allEntryIterator(files,entryIterator,with_progress=False,histo_step=102,opti
             else:
                 
                 if entryIterator == EcoPCRDBSequenceIterator and options is not None:
-                    if options.ecodb==f:
+                    if hasattr(options,'ecodb') and options.ecodb==f:
                         iterator = entryIterator(f,options.taxonomy)
                     else:
                         iterator = entryIterator(f)