diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index e9b4454c49c..7380b2c8434 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -714,23 +714,16 @@ class CustomTrack ( Tabular ):
         for hdr in headers:
             if first_line:
                 try:
-                    if hdr[0].startswith('track'):
-                        first_line = False
-                    else:
-                        return False
-                except:
-                    return False
+                    if hdr[0].startswith('track') and hdr[0].find('color') > -1 and hdr[0].find('visibility') > -1: first_line = False
+                    else: return False
+                except: return False
             else:     
                 try:
-                    if not (hdr[0] == '' or hdr[0].startswith( '#' )):
-                        if len(hdr) < 3:
-                            return False
-                        try:
-                            map( int, [hdr[1], hdr[2]] )
-                        except:
-                            return False
-                except:
-                    return False
+                    if hdr[0] and not hdr[0].startswith( '#' ):
+                        if len( hdr ) < 3: return False
+                        try: map( int, [hdr[1], hdr[2]] )
+                        except: return False
+                except: return False
         return True
 
 class GBrowseTrack ( Tabular ):
diff --git a/tools/new_operations/subtract_query.py b/tools/new_operations/subtract_query.py
index 7befb9b428e..39fb232dd32 100644
--- a/tools/new_operations/subtract_query.py
+++ b/tools/new_operations/subtract_query.py
@@ -18,12 +18,16 @@ def get_lines(fname, begin_col='', end_col=''):
     i = 0
     for i, line in enumerate(file(fname)):
         line = line.rstrip('\r\n')
-        if line != '' and not line.startswith('#'):
+        if line and not line.startswith('#'):
             if begin_col and end_col:
                 """Both begin_col and end_col must be integers at this point."""
-                line = line.split('\t')
-                line = '\t'.join([line[j] for j in range(begin_col-1, end_col)])
-            lines.add( line )
+                try:
+                    line = line.split('\t')
+                    line = '\t'.join([line[j] for j in range(begin_col-1, end_col)])
+                    lines.add( line )
+                except: pass
+            else:
+                lines.add( line )
     if i: return (i+1, lines)
     else: return (i, lines)
 
@@ -89,7 +93,7 @@ def main():
         info_msg += 'Restricted to columns c' + str(begin_col) + ' thru c' + str(end_col) + '. '
 
     if diff1 > 0:
-        info_msg += 'Eliminated %d duplicate/blank/comment lines from first query.' %diff1
+        info_msg += 'Eliminated %d duplicate/blank/comment/invalid lines from first query.' %diff1
     
     print info_msg