diff --git a/src/main/java/au/edu/wehi/idsv/DirectedEvidenceOrder.java b/src/main/java/au/edu/wehi/idsv/DirectedEvidenceOrder.java
index ee34606e..f08ab57a 100644
--- a/src/main/java/au/edu/wehi/idsv/DirectedEvidenceOrder.java
+++ b/src/main/java/au/edu/wehi/idsv/DirectedEvidenceOrder.java
@@ -2,7 +2,6 @@
 
 import com.google.common.collect.ComparisonChain;
 import com.google.common.collect.Ordering;
-import htsjdk.samtools.SAMRecord;
 
 import java.util.Comparator;
 
diff --git a/src/main/java/au/edu/wehi/idsv/debruijn/HighestWeightSimilarPath.java b/src/main/java/au/edu/wehi/idsv/debruijn/HighestWeightSimilarPath.java
index 6417a161..4daa4107 100644
--- a/src/main/java/au/edu/wehi/idsv/debruijn/HighestWeightSimilarPath.java
+++ b/src/main/java/au/edu/wehi/idsv/debruijn/HighestWeightSimilarPath.java
@@ -1,7 +1,6 @@
 package au.edu.wehi.idsv.debruijn;
 
 import au.edu.wehi.idsv.graph.WeightedSequenceGraphNodeUtil;
-import au.edu.wehi.idsv.util.AlgorithmRuntimeSafetyLimitExceededException;
 import au.edu.wehi.idsv.visualisation.NodeTraversalTracker;
 import com.google.common.collect.ImmutableList;
 import com.google.common.collect.Lists;
diff --git a/src/main/java/au/edu/wehi/idsv/util/AutoClosingMergedIterator.java b/src/main/java/au/edu/wehi/idsv/util/AutoClosingMergedIterator.java
index 4f8a88ca..55e540ff 100644
--- a/src/main/java/au/edu/wehi/idsv/util/AutoClosingMergedIterator.java
+++ b/src/main/java/au/edu/wehi/idsv/util/AutoClosingMergedIterator.java
@@ -2,9 +2,7 @@
 
 import au.edu.wehi.idsv.Defaults;
 import au.edu.wehi.idsv.validation.OrderAssertingIterator;
-import com.google.common.base.Function;
 import com.google.common.collect.Iterables;
-import com.google.common.collect.Iterators;
 import com.google.common.collect.Lists;
 import htsjdk.samtools.util.CloseableIterator;
 import htsjdk.samtools.util.CloserUtil;