diff --git a/src/index.rs b/src/index.rs
index 3747e6f5..0cb6a97d 100644
--- a/src/index.rs
+++ b/src/index.rs
@@ -1,4 +1,5 @@
 use sourmash::index::revindex::RevIndex;
+use sourmash::index::revindex::RevIndexOps;
 use sourmash::prelude::*;
 use std::path::Path;
 
@@ -10,6 +11,7 @@ pub fn index<P: AsRef<Path>>(
     output: P,
     colors: bool,
     allow_failed_sigpaths: bool,
+    use_internal_storage: bool,
 ) -> Result<(), Box<dyn std::error::Error>> {
     println!("Loading siglist");
 
@@ -20,11 +22,15 @@ pub fn index<P: AsRef<Path>>(
         allow_failed_sigpaths,
     )?;
 
-    RevIndex::create(
+    let mut index = RevIndex::create(
         output.as_ref(),
         collection.select(selection)?.try_into()?,
         colors,
     )?;
 
+    if use_internal_storage {
+        index.internalize_storage()?;
+    }
+
     Ok(())
 }
diff --git a/src/lib.rs b/src/lib.rs
index 4c1b7032..42fef4b8 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -179,10 +179,18 @@ fn do_index(
     moltype: String,
     output: String,
     colors: bool,
+    use_internal_storage: bool,
 ) -> anyhow::Result<u8> {
     let selection = build_selection(ksize, scaled, &moltype);
     let allow_failed_sigpaths = false;
-    match index::index(siglist, &selection, output, colors, allow_failed_sigpaths) {
+    match index::index(
+        siglist,
+        &selection,
+        output,
+        colors,
+        allow_failed_sigpaths,
+        use_internal_storage,
+    ) {
         Ok(_) => Ok(0),
         Err(e) => {
             eprintln!("Error: {e}");
diff --git a/src/python/sourmash_plugin_branchwater/__init__.py b/src/python/sourmash_plugin_branchwater/__init__.py
index 1e4240d2..1a5c3f9b 100755
--- a/src/python/sourmash_plugin_branchwater/__init__.py
+++ b/src/python/sourmash_plugin_branchwater/__init__.py
@@ -190,6 +190,12 @@ def __init__(self, p):
                        help = 'molecule type (DNA, protein, dayhoff, or hp; default DNA)')
         p.add_argument('-c', '--cores', default=0, type=int,
                        help='number of cores to use (default is all available)')
+        p.add_argument('--internal-storage', default=True, action='store_true',
+                       help="build indexes that contain sketches and are relocatable (default: True)")
+        p.add_argument('--no-internal-storage', '--no-store-sketches',
+                       action='store_false',
+                       help="do not store sketches in the index; index may not be relocatable (default: False)",
+                       dest='internal_storage')
 
     def main(self, args):
         notify(f"ksize: {args.ksize} / scaled: {args.scaled} / moltype: {args.moltype} ")
@@ -205,7 +211,8 @@ def main(self, args):
                                                       args.scaled,
                                                       args.moltype,
                                                       args.output,
-                                                      False) # colors - currently must be false?
+                                                      False, # colors - currently must be false?
+                                                      args.internal_storage)
         if status == 0:
             notify(f"...index is done! results in '{args.output}'")
         return status
@@ -217,7 +224,7 @@ class Branchwater_Check(CommandLinePlugin):
     def __init__(self, p):
         super().__init__(p)
         p.add_argument('index',
-                       help='index file')
+                       help="RocksDB index file created with 'index'")
         p.add_argument('--quick', action='store_true')
 
     def main(self, args):
diff --git a/src/python/tests/conftest.py b/src/python/tests/conftest.py
index 49ebcee7..052837f6 100644
--- a/src/python/tests/conftest.py
+++ b/src/python/tests/conftest.py
@@ -6,3 +6,20 @@
 def runtmp():
     with TempDirectory() as location:
         yield RunnerContext(location)
+
+
+@pytest.fixture(params=["--internal-storage", "--no-internal-storage"])
+def toggle_internal_storage(request):
+    return request.param
+
+@pytest.fixture(params=[True, False])
+def zip_query(request):
+    return request.param
+
+@pytest.fixture(params=[True, False])
+def zip_against(request):
+    return request.param
+
+@pytest.fixture(params=[True, False])
+def indexed(request):
+    return request.param
diff --git a/src/python/tests/test_index.py b/src/python/tests/test_index.py
index f490d2aa..69faf8ae 100644
--- a/src/python/tests/test_index.py
+++ b/src/python/tests/test_index.py
@@ -2,6 +2,7 @@
 import pytest
 import pandas
 import sourmash
+import shutil
 
 from . import sourmash_tst_utils as utils
 
@@ -24,7 +25,7 @@ def test_installed(runtmp):
     assert 'usage:  index' in runtmp.last_result.err
 
 
-def test_index(runtmp):
+def test_index(runtmp, toggle_internal_storage):
     # test basic index!
     siglist = runtmp.output('db-sigs.txt')
 
@@ -34,50 +35,52 @@ def test_index(runtmp):
 
     make_file_list(siglist, [sig2, sig47, sig63])
 
-    output = runtmp.output('db.rdb')
+    output = runtmp.output('db.rocksdb')
 
     runtmp.sourmash('scripts', 'index', siglist,
-                    '-o', output)
+                    '-o', output, toggle_internal_storage)
     assert os.path.exists(output)
     print(runtmp.last_result.err)
 
     assert 'index is done' in runtmp.last_result.err
 
 
-def test_index_protein(runtmp):
+def test_index_protein(runtmp, toggle_internal_storage):
     sigs = get_test_data('protein.zip')
     output = runtmp.output('db.rocksdb')
 
     runtmp.sourmash('scripts', 'index', sigs, '-k', '19', '-s', '100',
-                    '--moltype', 'protein', '-o', output)
+                    '--moltype', 'protein', '-o', output,
+                    toggle_internal_storage)
     assert os.path.exists(output)
     print(runtmp.last_result.err)
     assert 'index is done' in runtmp.last_result.err
 
 
-def test_index_dayhoff(runtmp):
+def test_index_dayhoff(runtmp, toggle_internal_storage):
     sigs = get_test_data('dayhoff.zip')
     output = runtmp.output('db.rocksdb')
 
     runtmp.sourmash('scripts', 'index', sigs, '-k', '19', '-s', '100',
-                    '--moltype', 'dayhoff', '-o', output)
+                    '--moltype', 'dayhoff', '-o', output,
+                    toggle_internal_storage)
     assert os.path.exists(output)
     print(runtmp.last_result.err)
     assert 'index is done' in runtmp.last_result.err
 
 
-def test_index_protein(runtmp):
+def test_index_protein(runtmp, toggle_internal_storage):
     sigs = get_test_data('hp.zip')
     output = runtmp.output('db.rocksdb')
 
     runtmp.sourmash('scripts', 'index', sigs, '-k', '19', '-s', '100',
-                    '--moltype', 'hp', '-o', output)
+                    '--moltype', 'hp', '-o', output, toggle_internal_storage)
     assert os.path.exists(output)
     print(runtmp.last_result.err)
     assert 'index is done' in runtmp.last_result.err
 
 
-def test_index_missing_siglist(runtmp, capfd):
+def test_index_missing_siglist(runtmp, capfd, toggle_internal_storage):
     # test missing siglist file
     siglist = runtmp.output('db-sigs.txt')
     output = runtmp.output('out.db')
@@ -85,21 +88,21 @@ def test_index_missing_siglist(runtmp, capfd):
 
     with pytest.raises(utils.SourmashCommandFailed):
         runtmp.sourmash('scripts', 'index', siglist,
-                        '-o', output)
+                        '-o', output, toggle_internal_storage)
 
     captured = capfd.readouterr()
     print(captured.err)
     assert 'Error: No such file or directory' in captured.err
 
 
-def test_index_sig(runtmp, capfd):
+def test_index_sig(runtmp, capfd, toggle_internal_storage):
     # test index with a .sig.gz file instead of pathlist
     # (should work now)
     sig2 = get_test_data('2.fa.sig.gz')
     output = runtmp.output('out.db')
 
     runtmp.sourmash('scripts', 'index', sig2,
-                        '-o', output)
+                    '-o', output, toggle_internal_storage)
 
     captured = capfd.readouterr()
     print(captured.err)
@@ -107,7 +110,7 @@ def test_index_sig(runtmp, capfd):
     assert 'index is done' in runtmp.last_result.err
 
 
-def test_index_manifest(runtmp, capfd):
+def test_index_manifest(runtmp, capfd, toggle_internal_storage):
     # test index with a manifest file
     sig2 = get_test_data('2.fa.sig.gz')
     output = runtmp.output('out.db')
@@ -115,7 +118,7 @@ def test_index_manifest(runtmp, capfd):
     runtmp.sourmash("sig", "manifest", sig2, "-o", sig_mf)
 
     runtmp.sourmash('scripts', 'index', sig_mf,
-                        '-o', output)
+                        '-o', output, toggle_internal_storage)
 
     captured = capfd.readouterr()
     print(captured.err)
@@ -132,7 +135,7 @@ def test_index_bad_siglist_2(runtmp, capfd):
     sig63 = get_test_data('63.fa.sig.gz')
     make_file_list(against_list, [sig2, "no-exist"])
 
-    db = runtmp.output('db.rdb')
+    db = runtmp.output('db.rocksdb')
 
     with pytest.raises(utils.SourmashCommandFailed):
         runtmp.sourmash('scripts', 'index', against_list,
@@ -164,7 +167,7 @@ def test_index_empty_siglist(runtmp, capfd):
 def test_index_nomatch(runtmp, capfd):
     # test index with a siglist file that has (only) a non-matching ksize sig
     siglist = runtmp.output('against.txt')
-    db = runtmp.output('db.rdb')
+    db = runtmp.output('db.rocksdb')
 
     sig1 = get_test_data('1.fa.k21.sig.gz')
     make_file_list(siglist, [sig1])
@@ -184,7 +187,7 @@ def test_index_nomatch(runtmp, capfd):
 def test_index_nomatch_sig_in_siglist(runtmp, capfd):
     # test index with a siglist file that has both matching and non-matching sigs
     siglist = runtmp.output('against.txt')
-    db = runtmp.output('db.rdb')
+    db = runtmp.output('db.rocksdb')
 
     sig2 = get_test_data('2.fa.sig.gz')
     sig1 = get_test_data('1.fa.k21.sig.gz')
@@ -201,7 +204,7 @@ def test_index_nomatch_sig_in_siglist(runtmp, capfd):
     assert os.path.exists(db)
 
 
-def test_index_zipfile(runtmp, capfd):
+def test_index_zipfile(runtmp, capfd, toggle_internal_storage):
     # test basic index from sourmash zipfile
     siglist = runtmp.output('db-sigs.txt')
 
@@ -215,10 +218,48 @@ def test_index_zipfile(runtmp, capfd):
 
     runtmp.sourmash('sig', 'cat', siglist, '-o', zipf)
 
-    output = runtmp.output('db.rdb')
+    output = runtmp.output('db.rocksdb')
+
+    runtmp.sourmash('scripts', 'index', zipf,
+                    '-o', output, toggle_internal_storage)
+    assert os.path.exists(output)
+    print(runtmp.last_result.err)
+
+    assert 'index is done' in runtmp.last_result.err
+    captured = capfd.readouterr()
+    print(captured.err)
+
+
+def test_index_zipfile_subdir(runtmp, capfd, toggle_internal_storage):
+    # test index from sourmash zipfile in different directory.
+
+    # this was a tough test to get to fail!! have to:
+    # * use non-abspath for zip file creation
+    # * use non-abspath to zip file for indexing
+    # so that the relative path gets things wrong.
+
+    siglist = runtmp.output('db-sigs.txt')
+
+    sig2 = get_test_data('2.fa.sig.gz')
+    sig47 = get_test_data('47.fa.sig.gz')
+    sig63 = get_test_data('63.fa.sig.gz')
+
+    shutil.copyfile(sig2, runtmp.output('2.fa.sig.gz'))
+    shutil.copyfile(sig47, runtmp.output('47.fa.sig.gz'))
+    shutil.copyfile(sig63, runtmp.output('63.fa.sig.gz'))
+
+    os.mkdir(runtmp.output('subdir'))
+
+    zipf = 'sigs.zip'
+
+    runtmp.sourmash('sig', 'cat', '2.fa.sig.gz', '47.fa.sig.gz',
+                    '63.fa.sig.gz', '-o', zipf)
+
+    output = runtmp.output('subdir/db.rocksdb')
 
     runtmp.sourmash('scripts', 'index', zipf,
-                    '-o', output)
+                    '-o', output, in_directory=runtmp.output(''),
+                    toggle_internal_storage=toggle_internal_storage)
     assert os.path.exists(output)
     print(runtmp.last_result.err)
 
@@ -226,8 +267,13 @@ def test_index_zipfile(runtmp, capfd):
     captured = capfd.readouterr()
     print(captured.err)
 
+    runtmp.sourmash('scripts', 'check', 'db.rocksdb',
+                    in_directory=runtmp.output('subdir'))
+    runtmp.sourmash('scripts', 'check', 'subdir/db.rocksdb',
+                    in_directory=runtmp.output(''))
 
-def test_index_zipfile_repeated_md5sums(runtmp, capfd):
+
+def test_index_zipfile_repeated_md5sums(runtmp, capfd, toggle_internal_storage):
     # test that we're reading all files, including repeated md5sums
     siglist = runtmp.output('db-sigs.txt')
 
@@ -242,10 +288,10 @@ def test_index_zipfile_repeated_md5sums(runtmp, capfd):
     zipf = runtmp.output('sigs.zip')
     runtmp.sourmash('sig', 'cat', siglist, '-o', zipf)
 
-    output = runtmp.output('db.rdb')
+    output = runtmp.output('db.rocksdb')
 
     runtmp.sourmash('scripts', 'index', zipf,
-                    '-o', output)
+                    '-o', output, toggle_internal_storage)
     assert os.path.exists(output)
     print(runtmp.last_result.err)
 
@@ -255,7 +301,7 @@ def test_index_zipfile_repeated_md5sums(runtmp, capfd):
     assert 'index is done' in runtmp.last_result.err
 
 
-def test_index_zipfile_multiparam(runtmp, capfd):
+def test_index_zipfile_multiparam(runtmp, capfd, toggle_internal_storage):
     # test index from sourmash zipfile with multiple ksizes / scaled /moltype
     siglist = runtmp.output('db-sigs.txt')
 
@@ -272,10 +318,10 @@ def test_index_zipfile_multiparam(runtmp, capfd):
 
     runtmp.sourmash('sig', 'cat', siglist, '-o', zipf)
 
-    output = runtmp.output('db.rdb')
+    output = runtmp.output('db.rocksdb')
 
     runtmp.sourmash('scripts', 'index', zipf,
-                    '-o', output)
+                    '-o', output, toggle_internal_storage)
     assert os.path.exists(output)
     print(runtmp.last_result.err)
 
@@ -306,7 +352,7 @@ def test_index_zipfile_bad(runtmp, capfd):
     assert "Couldn't find End Of Central Directory Record" in captured.err
 
 
-def test_index_check(runtmp):
+def test_index_check(runtmp, toggle_internal_storage):
     # test check index
     siglist = runtmp.output('db-sigs.txt')
 
@@ -315,10 +361,10 @@ def test_index_check(runtmp):
 
     make_file_list(siglist, [sig2, sig47])
 
-    output = runtmp.output('db.rdb')
+    output = runtmp.output('db.rocksdb')
 
     runtmp.sourmash('scripts', 'index', siglist,
-                    '-o', output)
+                    '-o', output, toggle_internal_storage)
 
     runtmp.sourmash('scripts', 'check', output)
     print(runtmp.last_result.err)
@@ -326,7 +372,7 @@ def test_index_check(runtmp):
     assert 'index is ok' in runtmp.last_result.err
 
 
-def test_index_check_quick(runtmp):
+def test_index_check_quick(runtmp, toggle_internal_storage):
     # test check index
     siglist = runtmp.output('db-sigs.txt')
 
@@ -335,12 +381,33 @@ def test_index_check_quick(runtmp):
 
     make_file_list(siglist, [sig2, sig47])
 
-    output = runtmp.output('db.rdb')
+    output = runtmp.output('db.rocksdb')
 
     runtmp.sourmash('scripts', 'index', siglist,
-                    '-o', output)
+                    '-o', output, toggle_internal_storage)
 
     runtmp.sourmash('scripts', 'check', '--quick', output)
     print(runtmp.last_result.err)
 
     assert 'index is ok' in runtmp.last_result.err
+
+
+def test_index_subdir(runtmp, toggle_internal_storage):
+    # test basic index & output to subdir
+    siglist = runtmp.output('db-sigs.txt')
+
+    sig2 = get_test_data('2.fa.sig.gz')
+    sig47 = get_test_data('47.fa.sig.gz')
+    sig63 = get_test_data('63.fa.sig.gz')
+
+    make_file_list(siglist, [sig2, sig47, sig63])
+
+    os.mkdir(runtmp.output('subdir'))
+    output = runtmp.output('subdir/db.rocksdb')
+
+    runtmp.sourmash('scripts', 'index', siglist,
+                    '-o', output, toggle_internal_storage)
+    assert os.path.exists(output)
+    print(runtmp.last_result.err)
+
+    runtmp.sourmash('scripts', 'check', output)
diff --git a/src/python/tests/test_multigather.py b/src/python/tests/test_multigather.py
index 132262d2..b3649ee9 100644
--- a/src/python/tests/test_multigather.py
+++ b/src/python/tests/test_multigather.py
@@ -21,11 +21,12 @@ def make_file_list(filename, paths):
         fp.write("\n")
 
 
-def index_siglist(runtmp, siglist, db, ksize=31, scaled=1000, moltype='DNA'):
+def index_siglist(runtmp, siglist, db, *, ksize=31, scaled=1000, moltype='DNA',
+                  toggle_internal_storage='--internal-storage'):
     # build index
     runtmp.sourmash('scripts', 'index', siglist,
                     '-o', db, '-k', str(ksize), '--scaled', str(scaled),
-                    '--moltype', moltype)
+                    '--moltype', moltype, toggle_internal_storage)
     return db
 
 
@@ -41,7 +42,6 @@ def zip_siglist(runtmp, siglist, db):
                     '-o', db)
     return db
 
-@pytest.mark.parametrize('zip_against', [False, True])
 def test_simple(runtmp, zip_against):
     # test basic execution!
     query = get_test_data('SRR606249.sig.gz')
@@ -203,8 +203,7 @@ def test_simple_read_manifests(runtmp):
     assert {'query_filename', 'query_name', 'query_md5', 'match_name', 'match_md5', 'intersect_bp', 'gather_result_rank'}.issubset(keys)
 
 
-@pytest.mark.parametrize('zip_query', [False, True])
-def test_simple_indexed(runtmp, zip_query):
+def test_simple_indexed(runtmp, zip_query, toggle_internal_storage):
     # test basic execution!
     query = get_test_data('SRR606249.sig.gz')
     sig2 = get_test_data('2.fa.sig.gz')
@@ -221,7 +220,7 @@ def test_simple_indexed(runtmp, zip_query):
         query_list = zip_siglist(runtmp, query_list, runtmp.output('query.zip'))
 
     g_output = runtmp.output('out.csv')
-    against_db = index_siglist(runtmp, against_list, runtmp.output('test.rocksdb'))
+    against_db = index_siglist(runtmp, against_list, runtmp.output('test.rocksdb'), toggle_internal_storage=toggle_internal_storage)
     runtmp.sourmash('scripts', 'fastmultigather', query_list,
                         against_db, '-s', '100000', '-t', '0',
                         '-o', g_output)
@@ -240,7 +239,7 @@ def test_simple_indexed(runtmp, zip_query):
     assert  keys == expected_keys
 
 
-def test_simple_indexed_query_manifest(runtmp):
+def test_simple_indexed_query_manifest(runtmp, toggle_internal_storage):
     # test basic execution!
     query = get_test_data('SRR606249.sig.gz')
     sig2 = get_test_data('2.fa.sig.gz')
@@ -254,7 +253,8 @@ def test_simple_indexed_query_manifest(runtmp):
     runtmp.sourmash("sig", "manifest", query, "-o", query_mf)
 
     g_output = runtmp.output('out.csv')
-    against_db = index_siglist(runtmp, against_list, runtmp.output('db'))
+    against_db = index_siglist(runtmp, against_list, runtmp.output('db'),
+                               toggle_internal_storage=toggle_internal_storage)
     runtmp.sourmash('scripts', 'fastmultigather', query_mf,
                         against_db, '-s', '100000', '-t', '0',
                         '-o', g_output)
@@ -273,9 +273,7 @@ def test_simple_indexed_query_manifest(runtmp):
     assert  keys == expected_keys
 
 
-@pytest.mark.parametrize('zip_query', [False, True])
-@pytest.mark.parametrize('indexed', [False, True])
-def test_missing_querylist(runtmp, capfd, indexed, zip_query):
+def test_missing_querylist(runtmp, capfd, indexed, zip_query, toggle_internal_storage):
     # test missing querylist
     query_list = runtmp.output('query.txt')
     against_list = runtmp.output('against.txt')
@@ -290,7 +288,8 @@ def test_missing_querylist(runtmp, capfd, indexed, zip_query):
     make_file_list(against_list, [sig2, sig47, sig63])
 
     if indexed:
-        against_list = index_siglist(runtmp, against_list, runtmp.output('db'))
+        against_list = index_siglist(runtmp, against_list, runtmp.output('db'),
+                                     toggle_internal_storage=toggle_internal_storage)
 
     with pytest.raises(utils.SourmashCommandFailed):
         runtmp.sourmash('scripts', 'fastmultigather', query_list, against_list,
@@ -301,7 +300,6 @@ def test_missing_querylist(runtmp, capfd, indexed, zip_query):
     assert 'Error: No such file or directory' in captured.err
 
 
-@pytest.mark.parametrize('indexed', [False, True])
 def test_sig_query(runtmp, capfd, indexed):
     # sig file is now fine as a query
     query = get_test_data('SRR606249.sig.gz')
@@ -347,7 +345,6 @@ def test_sig_query(runtmp, capfd, indexed):
         assert {'query_filename', 'query_name', 'query_md5', 'match_name', 'match_md5', 'gather_result_rank', 'intersect_bp'}.issubset(keys)
 
 
-@pytest.mark.parametrize('indexed', [False, True])
 def test_bad_query(runtmp, capfd, indexed):
     # test with a bad query (a .sig.gz file renamed as zip file)
     against_list = runtmp.output('against.txt')
@@ -376,7 +373,6 @@ def test_bad_query(runtmp, capfd, indexed):
     assert "InvalidArchive" in captured.err
 
 
-@pytest.mark.parametrize('indexed', [False, True])
 def test_missing_query(runtmp, capfd, indexed):
     # test missing query
     query_list = runtmp.output('query.txt')
@@ -401,8 +397,6 @@ def test_missing_query(runtmp, capfd, indexed):
     assert "WARNING: 1 query paths failed to load. See error messages above."
 
 
-@pytest.mark.parametrize('indexed', [False, True])
-@pytest.mark.parametrize("zip_query", [False, True])
 def test_nomatch_query(runtmp, capfd, indexed, zip_query):
     # test nomatch file in querylist
     query_list = runtmp.output('query.txt')
@@ -429,7 +423,6 @@ def test_nomatch_query(runtmp, capfd, indexed, zip_query):
     assert "WARNING: skipped 1 query paths - no compatible signatures." in captured.err
 
 
-@pytest.mark.parametrize('zip_against', [False, True])
 def test_missing_against(runtmp, capfd, zip_against):
     # test missing against
     query_list = runtmp.output('query.txt')
@@ -506,7 +499,6 @@ def test_bad_against(runtmp, capfd):
     assert "WARNING: 1 search paths failed to load. See error messages above." in captured.err
 
 
-@pytest.mark.parametrize('zip_query', [False, True])
 def test_bad_against_2(runtmp, capfd, zip_query):
     # test with a bad against (a .sig.gz file renamed as zip file)
     query = get_test_data('SRR606249.sig.gz')
@@ -553,7 +545,6 @@ def test_empty_against(runtmp, capfd):
     assert "No search signatures loaded, exiting." in captured.err
 
 
-@pytest.mark.parametrize('zip_against', [False, True])
 def test_nomatch_in_against(runtmp, capfd, zip_against):
     # test an against file that has a non-matching ksize sig in it
     query = get_test_data('SRR606249.sig.gz')
@@ -578,7 +569,6 @@ def test_nomatch_in_against(runtmp, capfd, zip_against):
     assert 'WARNING: skipped 1 search paths - no compatible signatures.' in captured.err
 
 
-@pytest.mark.parametrize('zip_query', [False, True])
 def test_md5(runtmp, zip_query):
     # test correct md5s present in output
     query = get_test_data('SRR606249.sig.gz')
@@ -633,7 +623,6 @@ def test_md5(runtmp, zip_query):
             assert ss.md5sum() in md5s
 
 
-@pytest.mark.parametrize('zip_query', [False, True])
 def test_md5_indexed(runtmp, zip_query):
     # test correct md5s present in output
     query = get_test_data('SRR606249.sig.gz')
@@ -676,8 +665,6 @@ def test_md5_indexed(runtmp, zip_query):
             assert ss.md5sum() in md5s
 
 
-@pytest.mark.parametrize('zip_query', [False, True])
-@pytest.mark.parametrize('zip_against', [False, True])
 def test_csv_columns_vs_sourmash_prefetch(runtmp, zip_query, zip_against):
     # the column names should be strict subsets of sourmash prefetch cols
     query = get_test_data('SRR606249.sig.gz')
@@ -1145,8 +1132,8 @@ def test_nonindexed_full_vs_sourmash_gather(runtmp):
     assert fmg_total_weighted_hashes == g_total_weighted_hashes == set([73489])
 
 
-def test_rocksdb_no_sigs(runtmp, capfd):
-    # make sure fastmultigather error-exits if a gather fails.
+def test_rocksdb_gather_against_index_with_sigs(runtmp, capfd):
+    # fastmultigather should succeed if indexed sigs are stored internally.
     query = get_test_data('SRR606249.sig.gz')
 
     sig2 = get_test_data('2.fa.sig.gz')
@@ -1163,10 +1150,45 @@ def test_rocksdb_no_sigs(runtmp, capfd):
                                   "47.fa.sig.gz",
                                   "63.fa.sig.gz"])
 
-    # index!
+    # index! note: '--internal-storage' defaults to True
     runtmp.sourmash('scripts', 'index', against_list,
                     '-o', 'subdir/against.rocksdb')
 
+    # remove the external storage out from under the rocksdb.
+    os.unlink(runtmp.output('2.fa.sig.gz'))
+    os.unlink(runtmp.output('47.fa.sig.gz'))
+    os.unlink(runtmp.output('63.fa.sig.gz'))
+
+    g_output = runtmp.output('zzz.csv')
+
+    runtmp.sourmash('scripts', 'fastmultigather', query_list,
+                    'subdir/against.rocksdb', '-s', '100000', '-t', '0',
+                    '-o', g_output,
+                    in_location=runtmp.output(''))
+
+
+def test_rocksdb_no_internal_storage_gather_fails(runtmp, capfd):
+    # force gather to fail b/c we make an index with no internal sketches
+    query = get_test_data('SRR606249.sig.gz')
+
+    sig2 = get_test_data('2.fa.sig.gz')
+    sig47 = get_test_data('47.fa.sig.gz')
+    sig63 = get_test_data('63.fa.sig.gz')
+    shutil.copyfile(sig2, runtmp.output('2.fa.sig.gz'))
+    shutil.copyfile(sig47, runtmp.output('47.fa.sig.gz'))
+    shutil.copyfile(sig63, runtmp.output('63.fa.sig.gz'))
+
+    query_list = runtmp.output('query.txt')
+    make_file_list(query_list, [query])
+    against_list = runtmp.output('against.txt')
+    make_file_list(against_list, ["2.fa.sig.gz",
+                                  "47.fa.sig.gz",
+                                  "63.fa.sig.gz"])
+
+    # index!
+    runtmp.sourmash('scripts', 'index', against_list, '--no-internal-storage',
+                    '-o', 'subdir/against.rocksdb')
+
     # remove the external storage out from under the rocksdb.
     # this will make gather fail.
     os.unlink(runtmp.output('2.fa.sig.gz'))