Report error if species tree inference fails, resolves #919

scripts_of/__main__.py

@@ -1048,6 +1048,9 @@ def BetweenCoreOrthogroupsWorkflow(continuationDir, speciesInfoObj, seqsInfo, op
         core_rooted_species_tree = tree.Tree(files.FileHandler.GetCoreSpeciesTreeIDsRootedFN(), format=1)
         species_to_speices_map = lambda x: x
         rooted_species_tree_ids, qHaveSupport = trees2ologs_of.CheckAndRootTree(species_tree_unrooted_fn, core_rooted_species_tree, species_to_speices_map)
+        if rooted_species_tree_ids is None:
+            print("ERROR: Species tree inference failed. Please check for errors and check the species tree files: \n%s \n%s" % (species_tree_unrooted_fn, core_rooted_species_tree))
+            util.Fail()
         rooted_species_tree_fn = files.FileHandler.GetSpeciesTreeIDsRootedFN()
         rooted_species_tree_ids.write(outfile=rooted_species_tree_fn)
 

scripts_of/trees2ologs_of.py

@@ -714,7 +714,8 @@ def CheckAndRootTree(treeFN, species_tree_rooted, GeneToSpecies):
     Root tree
     Returns None if this fails, i.e. checks: exists, has more than one gene, can be rooted
     """
-    if (not os.path.exists(treeFN)) or os.stat(treeFN).st_size == 0: return None, False
+    if (not os.path.exists(treeFN)) or os.stat(treeFN).st_size == 0:
+        return None, False
     qHaveSupport = False
     try:
         tree = tree_lib.Tree(treeFN, format=2)
@@ -724,9 +725,11 @@ def CheckAndRootTree(treeFN, species_tree_rooted, GeneToSpecies):
             tree = tree_lib.Tree(treeFN)
         except:
             tree = tree_lib.Tree(treeFN, format=3)
-    if len(tree) == 1: return None, False
+    if len(tree) == 1:
+        return None, False
     root = GetRoot(tree, species_tree_rooted, GeneToSpecies)
-    if root == None: return None, False
+    if root == None:
+        return None, False
     # Pick the first root for now
     if root != tree:
         tree.set_outgroup(root)