diff --git a/api/src/org/labkey/api/util/FileUtil.java b/api/src/org/labkey/api/util/FileUtil.java
index 8446e0c3535..40dc5348e69 100644
--- a/api/src/org/labkey/api/util/FileUtil.java
+++ b/api/src/org/labkey/api/util/FileUtil.java
@@ -61,6 +61,7 @@
 import java.nio.CharBuffer;
 import java.nio.channels.FileChannel;
 import java.nio.channels.FileLock;
+import java.nio.channels.OverlappingFileLockException;
 import java.nio.channels.ReadableByteChannel;
 import java.nio.file.FileSystems;
 import java.nio.file.FileVisitResult;
@@ -1078,6 +1079,17 @@ public static void copyFile(File src, File dst) throws IOException
         }
     }
 
+    private static FileLock acquireLock(FileChannel out) throws IOException
+    {
+        try
+        {
+            return out.lock();
+        }
+        catch (OverlappingFileLockException e)
+        {
+            throw new IOException(e);
+        }
+    }
 
     // FileUtil.copyFile() does not use transferTo() or sync()
     public static void copyFile(ReadableByteChannel in, long expected, File dst) throws IOException
@@ -1092,7 +1104,7 @@ public static void copyFile(ReadableByteChannel in, long expected, File dst) thr
 
         try (FileOutputStream os = new FileOutputStream(dst);
              FileChannel out = os.getChannel();
-             FileLock lockOut = out.lock())
+             FileLock lockOut = acquireLock(out))
         {
             do
             {
diff --git a/experiment/src/org/labkey/experiment/api/SampleTypeServiceImpl.java b/experiment/src/org/labkey/experiment/api/SampleTypeServiceImpl.java
index b9b43484560..46e14260387 100644
--- a/experiment/src/org/labkey/experiment/api/SampleTypeServiceImpl.java
+++ b/experiment/src/org/labkey/experiment/api/SampleTypeServiceImpl.java
@@ -118,6 +118,7 @@
 import java.util.Optional;
 import java.util.Set;
 import java.util.SortedSet;
+import java.util.TreeMap;
 import java.util.TreeSet;
 import java.util.function.Function;
 import java.util.function.Predicate;
@@ -1700,7 +1701,7 @@ private Map<Integer, Pair<Integer, String>> getSampleAliquotCounts(Collection<In
                 .append(")-1 AS CreatedAliquotCount FROM exp.material AS m WHERE m.rowid\s");
         dialect.appendInClauseSql(sql, sampleIds);
 
-        Map<Integer, Pair<Integer, String>> sampleAliquotCounts = new HashMap<>();
+        Map<Integer, Pair<Integer, String>> sampleAliquotCounts = new TreeMap<>(); // Order sample by rowId to reduce probability of deadlock with search indexer
         try (ResultSet rs = new SqlSelector(dbSchema, sql).getResultSet())
         {
             while (rs.next())
@@ -1761,7 +1762,7 @@ SELECT RootMaterialRowId as rootRowId, COUNT(*) as aliquotCount
         }
         dialect.appendInClauseSql(sql, sampleIds);
 
-        Map<Integer, Pair<Integer, String>> sampleAliquotCounts = new HashMap<>();
+        Map<Integer, Pair<Integer, String>> sampleAliquotCounts = new TreeMap<>(); // Order by rowId to reduce deadlock with search indexer
         try (ResultSet rs = new SqlSelector(dbSchema, sql).getResultSet())
         {
             while (rs.next())