diff --git a/nesoni/CHANGES b/nesoni/CHANGES
index 73935f9..eed2dea 100644
--- a/nesoni/CHANGES
+++ b/nesoni/CHANGES
@@ -1,4 +1,7 @@
 
+0.132 - link_up_annotations forgiving of duplicated ID if ID not used.
+        Execute can have a specified location for state and log files.
+
 0.131 - Log transformation is now performed using Varistran.
         Ignore spurious whitespace when loading GFF files.
         Default to norm factors of 1 if calcNormFactors fails
diff --git a/nesoni/__init__.py b/nesoni/__init__.py
index cde3d61..220b92a 100644
--- a/nesoni/__init__.py
+++ b/nesoni/__init__.py
@@ -1,4 +1,4 @@
-VERSION='0.131'
+VERSION='0.132'
 #^ Note: this first line is read by the setup.py script to get the version
 
 import sys
diff --git a/nesoni/annotation.py b/nesoni/annotation.py
index 7ecb43c..988e97e 100644
--- a/nesoni/annotation.py
+++ b/nesoni/annotation.py
@@ -176,18 +176,23 @@ def get_seq(self, seq_dict):
 def link_up_annotations(annotations):
     """ Link up GFF3 annotations using parent/child relationships """
     index = { }
+    bad = set()
     for item in annotations:
         item.children = [ ]
         if 'ID' not in item.attr: continue
         ID = item.attr['ID']
-        assert ID not in index, 'Annotations contain a duplicated ID: '+ID
+        #assert ID not in index, 'Annotations contain a duplicated ID: '+ID
+        if ID in index: 
+            bad.add(ID)
         index[ID] = item
         
     for item in annotations:
         if 'Parent' not in item.attr:
             item.parents = [ ]
         else:
-            item.parents = [ index[parent_id] for parent_id in item.attr['Parent'].split(',') ]
+            parent_ids = item.attr['Parent'].split(',')
+            assert bad.isdisjoint(parent_ids), "Duplicate ID used as Parent in GFF file: "+",".join(bad&set(parent_ids))
+            item.parents = [ index[parent_id] for parent_id in parent_ids if parent_id in index ]
             for parent in item.parents:
                 parent.children.append(item)
                 
@@ -388,6 +393,9 @@ def write_gff3_header(f):
     print >> f, '##gff-version 3'
 
 def write_gff3(filename, items):
+    # IGV likes to index large GFFs, and needs them to be sorted for this
+    items = sorted(items, key=lambda item: (item.seqid, item.start))
+    
     with io.open_possibly_compressed_writer(filename) as f:
         write_gff3_header(f)
         for item in items:
diff --git a/nesoni/legion.py b/nesoni/legion.py
index 684c515..96d29e1 100644
--- a/nesoni/legion.py
+++ b/nesoni/legion.py
@@ -967,6 +967,7 @@ def process_make(action, stage=None):
 """)
 @config.Int_flag('cores','Advise how many cores the command will use.', 
     affects_output=False)
+@config.String_flag('prefix','Location of state and log files.')
 @config.Main_section('command','Command to execute', allow_flags=True, empty_is_ok=False)
 @config.Section('execution_options',
     'Extra options to add to start of command, eg to set the number of cores to use. '
@@ -976,6 +977,19 @@ class Execute(config.Action_filter):
     cores = 1
     command = [ ]
     execution_options = [ ]
+    prefix = None
+
+
+    def log_filename(self):
+        if self.prefix is None: 
+            return None
+        return self.prefix + '_log.txt'
+
+    def state_filename(self):
+        if self.prefix is None: 
+            return super(Execute,self).state_filename()
+        return self.prefix + '.state'
+    
 
     def cores_required(self):
         return self.cores
diff --git a/nesoni/nesoni-r/R/counts.R b/nesoni/nesoni-r/R/counts.R
index 2fc1447..5a1ced5 100644
--- a/nesoni/nesoni-r/R/counts.R
+++ b/nesoni/nesoni-r/R/counts.R
@@ -51,7 +51,7 @@ read.counts <- function(filename, min.total=0, min.max=0, keep=NULL, norm.file=N
     if (!quiet && (min.total > 0 || min.max > 0))
         cat(sprintf("%d genes after filtering\n", sum(good)))
     
-    result <- DGEList(counts=counts[good,], gene=gene[good,])
+    result <- DGEList(counts=counts[good,], genes=gene[good,])
 
     mean.lib.size <- exp(mean(log(result$samples$lib.size)))
 
diff --git a/nesoni/nesoni-r/R/nesoni_version.R b/nesoni/nesoni-r/R/nesoni_version.R
index b6bf564..48ee958 100644
--- a/nesoni/nesoni-r/R/nesoni_version.R
+++ b/nesoni/nesoni-r/R/nesoni_version.R
@@ -1,2 +1,2 @@
 #Autogenerated
-nesoni_version <- function() { '0.130' }
+nesoni_version <- function() { '0.132' }