DuplicateKeyError: E11000 duplicate key error collection: virtool.indexes index: version_1 dup key: { : 0 }
https://sentry.io/cph/server/issues/562788089/

```
DuplicateKeyError: E11000 duplicate key error collection: virtool.indexes index: version_1 dup key: { : 0 }
(10 additional frame(s) were not displayed)
...
  File "pymongo/collection.py", line 682, in insert_one
    session=session),
  File "pymongo/collection.py", line 598, in _insert
    bypass_doc_val, session)
  File "pymongo/collection.py", line 579, in _insert_one
    _check_write_command_response(result)
  File "pymongo/helpers.py", line 208, in _check_write_command_response
    _raise_last_write_error(write_errors)
  File "pymongo/helpers.py", line 189, in _raise_last_write_error
    raise DuplicateKeyError(error.get("errmsg"), 11000, error)

Error handling request
```

Results in an a `500` error on index build request (#690).
diff --git a/virtool/app.py b/virtool/app.py
index 33f252936..b6d213165 100644
--- a/virtool/app.py
+++ b/virtool/app.py
@@ -142,7 +142,8 @@ async def init_check_db(app):
     await db.history.create_index("otu.id")
     await db.history.create_index("index.id")
     await db.history.create_index("created_at")
-    await db.indexes.create_index("version", unique=True)
+    await db.history.drop_indexes()
+    await db.indexes.create_index([("version", 1), ("reference.id", 1)], unique=True)
     await db.keys.create_index("id", unique=True)
     await db.keys.create_index("user.id")
     await db.samples.create_index([("created_at", pymongo.DESCENDING)])
['virtool/app.py']