2 files changed, 4 insertions, 3 deletions

diff --git a/src/main/java/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java
index a2676e8..2610652 100644
--- a/src/main/java/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java
@@ -1,6 +1,7 @@
 package uk.ac.ox.cs.pagoda.rules;
 
 import org.apache.commons.io.FilenameUtils;
+import org.semanticweb.HermiT.Configuration;
 import org.semanticweb.HermiT.Reasoner;
 import org.semanticweb.HermiT.model.*;
 import org.semanticweb.owlapi.model.*;
@@ -149,7 +150,7 @@ class ClassifyThread extends Thread {
         public void run() {
                 ontology = m_program.getOntology();
                 try {
-                        hermitReasoner = new Reasoner(ontology);
+                        hermitReasoner = new Reasoner(new Configuration(), ontology);
                         Timer t = new Timer(); 
                         hermitReasoner.classifyClasses();
                         Utility.logInfo("HermiT classification done: " + t.duration());
@@ -235,4 +236,4 @@ class ClassifyThread extends Thread {
         private Atom getAtom(OWLClass c) {
                 return Atom.create(AtomicConcept.create(c.toStringID()), X);
         }
-}
\ No newline at end of file
+}
diff --git a/src/main/java/uk/ac/ox/cs/pagoda/rules/Program.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/Program.java
index de06f52..22eb9ec 100644
--- a/src/main/java/uk/ac/ox/cs/pagoda/rules/Program.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/Program.java
@@ -273,7 +273,7 @@ protected PredicateDependency dependencyGraph;
                 Utility.logInfo("The number of data property range axioms that are ignored: " + noOfDataPropertyRangeAxioms + "(" + noOfAxioms + ")");
 
         DLOntology dlOntology = (DLOntology) clausifier.preprocessAndClausify(filteredOntology, null)[1];
-        dlClauses = dlOntology.getDLClauses();
+        dlClauses = new HashSet<DLClause>(dlOntology.getDLClauses());
         positiveFacts = dlOntology.getPositiveFacts();
         }