diff --git a/src/python/tests/test_gather.py b/src/python/tests/test_gather.py
index c777821a..1b90e0da 100644
--- a/src/python/tests/test_gather.py
+++ b/src/python/tests/test_gather.py
@@ -669,8 +669,8 @@ def test_simple_with_manifest_loading(runtmp):
     sig63 = get_test_data('63.fa.sig.gz')
 
     make_file_list(against_list, [sig2, sig47, sig63])
-    query_manifest = get_test_data("query-manifest.csv")
-    against_manifest = get_test_data("against-manifest.csv")
+    query_manifest = runtmp.output("qmf.csv")
+    against_manifest = runtmp.output("against-manifest.csv")
 
     runtmp.sourmash("sig", "manifest", query, "-o", query_manifest)
     runtmp.sourmash("sig", "manifest", against_list, "-o", against_manifest)
@@ -685,4 +685,4 @@ def test_simple_with_manifest_loading(runtmp):
     df = pandas.read_csv(g_output)
     assert len(df) == 3
     keys = set(df.keys())
-    assert keys == {'query_filename', 'query_name', 'query_md5', 'match_name', 'match_md5', 'rank', 'intersect_bp'}
+    assert {'query_filename', 'query_name', 'query_md5', 'match_name', 'match_md5', 'rank', 'intersect_bp'}.issubset(keys)
diff --git a/src/python/tests/test_multigather.py b/src/python/tests/test_multigather.py
index 5b40d548..7bc19dbb 100644
--- a/src/python/tests/test_multigather.py
+++ b/src/python/tests/test_multigather.py
@@ -255,7 +255,7 @@ def test_simple_indexed_query_manifest(runtmp):
     df = pandas.read_csv(g_output)
     assert len(df) == 3
     keys = set(df.keys())
-    assert keys == {'query_name', 'query_md5', 'match_name', 'match_md5', 'f_match_query', 'intersect_bp'}
+    assert {'query_name', 'query_md5', 'match_name', 'match_md5', 'f_match_query', 'intersect_bp'}.issubset(keys)
 
 
 @pytest.mark.parametrize('zip_query', [False, True])