diff --git a/Cargo.lock b/Cargo.lock
index 71111003..4d3fa303 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1596,7 +1596,7 @@ dependencies = [
 
 [[package]]
 name = "sourmash_plugin_branchwater"
-version = "0.9.8"
+version = "0.9.9-dev"
 dependencies = [
  "anyhow",
  "assert_cmd",
diff --git a/Cargo.toml b/Cargo.toml
index 0f86560e..85e3413e 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "sourmash_plugin_branchwater"
-version = "0.9.8"
+version = "0.9.9-dev"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
diff --git a/src/fastgather.rs b/src/fastgather.rs
index 4feff7cf..025ffc16 100644
--- a/src/fastgather.rs
+++ b/src/fastgather.rs
@@ -14,14 +14,14 @@ pub fn fastgather(
     against_filepath: String,
     threshold_bp: usize,
     scaled: usize,
-    selection: &Selection,
+    selection: Selection,
     gather_output: Option<String>,
     prefetch_output: Option<String>,
     allow_failed_sigpaths: bool,
 ) -> Result<()> {
     let query_collection = load_collection(
         &query_filepath,
-        selection,
+        &selection,
         ReportType::Query,
         allow_failed_sigpaths,
     )?;
@@ -40,7 +40,7 @@ pub fn fastgather(
     let query_md5 = query_sig.md5sum();
 
     // clone here is necessary b/c we use full query_sig in consume_query_by_gather
-    let query_sig_ds = query_sig.select(selection)?; // downsample
+    let query_sig_ds = query_sig.select(&selection)?; // downsample
     let query_mh = match query_sig_ds.try_into() {
         Ok(query_mh) => query_mh,
         Err(_) => {
@@ -50,7 +50,7 @@ pub fn fastgather(
     // load collection to match against.
     let against_collection = load_collection(
         &against_filepath,
-        selection,
+        &selection,
         ReportType::Against,
         allow_failed_sigpaths,
     )?;
diff --git a/src/fastmultigather.rs b/src/fastmultigather.rs
index 1fa37215..fa5295f8 100644
--- a/src/fastmultigather.rs
+++ b/src/fastmultigather.rs
@@ -29,8 +29,8 @@ pub fn fastmultigather(
     query_filepath: String,
     against_filepath: String,
     threshold_bp: usize,
-    scaled: usize,
-    selection: &Selection,
+    scaled: Option<usize>,
+    selection: Selection,
     allow_failed_sigpaths: bool,
     save_matches: bool,
     create_empty_results: bool,
@@ -40,11 +40,26 @@ pub fn fastmultigather(
     // load query collection
     let query_collection = load_collection(
         &query_filepath,
-        selection,
+        &selection,
         ReportType::Query,
         allow_failed_sigpaths,
     )?;
 
+    let scaled = match scaled {
+        Some(s) => s,
+        None => {
+            let scaled = query_collection.max_scaled().expect("no records!?").clone() as usize;
+            eprintln!(
+                "Setting scaled={} based on max scaled in query collection",
+                scaled
+            );
+            scaled
+        }
+    };
+
+    let mut against_selection = selection;
+    against_selection.set_scaled(scaled as u32);
+
     let threshold_hashes: u64 = {
         let x = threshold_bp / scaled;
         if x > 0 {
@@ -60,12 +75,12 @@ pub fn fastmultigather(
     // load against collection
     let against_collection = load_collection(
         &against_filepath,
-        selection,
+        &against_selection,
         ReportType::Against,
         allow_failed_sigpaths,
     )?;
     // load against sketches into memory, downsampling on the way
-    let against = against_collection.load_sketches(selection)?;
+    let against = against_collection.load_sketches(&against_selection)?;
 
     // Iterate over all queries => do prefetch and gather!
     let processed_queries = AtomicUsize::new(0);
diff --git a/src/index.rs b/src/index.rs
index c303b09b..102892fd 100644
--- a/src/index.rs
+++ b/src/index.rs
@@ -8,7 +8,7 @@ use sourmash::collection::{Collection, CollectionSet};
 
 pub fn index<P: AsRef<Path>>(
     siglist: String,
-    selection: &Selection,
+    selection: Selection,
     output: P,
     colors: bool,
     allow_failed_sigpaths: bool,
@@ -18,7 +18,7 @@ pub fn index<P: AsRef<Path>>(
 
     let multi = match load_collection(
         &siglist,
-        selection,
+        &selection,
         ReportType::General,
         allow_failed_sigpaths,
     ) {
@@ -31,7 +31,7 @@ pub fn index<P: AsRef<Path>>(
     let collection = match Collection::try_from(multi.clone()) {
         // conversion worked!
         Ok(c) => {
-            let cs: CollectionSet = c.select(selection)?.try_into()?;
+            let cs: CollectionSet = c.select(&selection)?.try_into()?;
             Ok(cs)
         }
         // conversion failed; can we/should we load it into memory?
@@ -39,7 +39,7 @@ pub fn index<P: AsRef<Path>>(
             if use_internal_storage {
                 eprintln!("WARNING: loading all sketches into memory in order to index.");
                 eprintln!("See 'index' documentation for details.");
-                let c: Collection = multi.load_all_sigs(selection)?;
+                let c: Collection = multi.load_all_sigs(&selection)?;
                 let cs: CollectionSet = c.try_into()?;
                 Ok(cs)
             } else {
diff --git a/src/lib.rs b/src/lib.rs
index d4bf33f5..68f869af 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -39,7 +39,7 @@ fn do_manysearch(
     ignore_abundance: Option<bool>,
 ) -> anyhow::Result<u8> {
     let againstfile_path: PathBuf = siglist_path.clone().into();
-    let selection = build_selection(ksize, scaled, &moltype);
+    let selection = build_selection(ksize, Some(scaled), &moltype);
     eprintln!("selection scaled: {:?}", selection.scaled());
     let allow_failed_sigpaths = true;
 
@@ -51,7 +51,7 @@ fn do_manysearch(
         match mastiff_manysearch::mastiff_manysearch(
             querylist_path,
             againstfile_path,
-            &selection,
+            selection,
             threshold,
             output_path,
             allow_failed_sigpaths,
@@ -66,7 +66,7 @@ fn do_manysearch(
         match manysearch::manysearch(
             querylist_path,
             siglist_path,
-            &selection,
+            selection,
             threshold,
             output_path,
             allow_failed_sigpaths,
@@ -94,7 +94,7 @@ fn do_fastgather(
     output_path_prefetch: Option<String>,
     output_path_gather: Option<String>,
 ) -> anyhow::Result<u8> {
-    let selection = build_selection(ksize, scaled, &moltype);
+    let selection = build_selection(ksize, Some(scaled), &moltype);
     let allow_failed_sigpaths = true;
 
     match fastgather::fastgather(
@@ -102,7 +102,7 @@ fn do_fastgather(
         siglist_path,
         threshold_bp,
         scaled,
-        &selection,
+        selection,
         output_path_prefetch,
         output_path_gather,
         allow_failed_sigpaths,
@@ -123,7 +123,7 @@ fn do_fastmultigather(
     siglist_path: String,
     threshold_bp: usize,
     ksize: u8,
-    scaled: usize,
+    scaled: Option<usize>,
     moltype: String,
     output_path: Option<String>,
     save_matches: bool,
@@ -138,7 +138,7 @@ fn do_fastmultigather(
         match mastiff_manygather::mastiff_manygather(
             query_filenames,
             againstfile_path,
-            &selection,
+            selection.clone(),
             threshold_bp,
             output_path,
             allow_failed_sigpaths,
@@ -158,7 +158,7 @@ fn do_fastmultigather(
             siglist_path,
             threshold_bp,
             scaled,
-            &selection,
+            selection,
             allow_failed_sigpaths,
             save_matches,
             create_empty_results,
@@ -199,11 +199,11 @@ fn do_index(
     colors: bool,
     use_internal_storage: bool,
 ) -> anyhow::Result<u8> {
-    let selection = build_selection(ksize, scaled, &moltype);
+    let selection = build_selection(ksize, Some(scaled), &moltype);
     let allow_failed_sigpaths = false;
     match index::index(
         siglist,
-        &selection,
+        selection,
         output,
         colors,
         allow_failed_sigpaths,
@@ -237,7 +237,7 @@ fn do_multisearch(
     siglist_path: String,
     threshold: f64,
     ksize: u8,
-    scaled: usize,
+    scaled: Option<usize>,
     moltype: String,
     estimate_ani: bool,
     output_path: Option<String>,
@@ -251,7 +251,7 @@ fn do_multisearch(
         querylist_path,
         siglist_path,
         threshold,
-        &selection,
+        selection,
         allow_failed_sigpaths,
         estimate_ani,
         output_path,
@@ -277,12 +277,12 @@ fn do_pairwise(
     write_all: bool,
     output_path: Option<String>,
 ) -> anyhow::Result<u8> {
-    let selection = build_selection(ksize, scaled, &moltype);
+    let selection = build_selection(ksize, Some(scaled), &moltype);
     let allow_failed_sigpaths = true;
     match pairwise::pairwise(
         siglist_path,
         threshold,
-        &selection,
+        selection,
         allow_failed_sigpaths,
         estimate_ani,
         write_all,
diff --git a/src/manysearch.rs b/src/manysearch.rs
index 1b77cb16..4c539267 100644
--- a/src/manysearch.rs
+++ b/src/manysearch.rs
@@ -19,7 +19,7 @@ use sourmash::sketch::minhash::KmerMinHash;
 pub fn manysearch(
     query_filepath: String,
     against_filepath: String,
-    selection: &Selection,
+    selection: Selection,
     threshold: f64,
     output: Option<String>,
     allow_failed_sigpaths: bool,
@@ -28,18 +28,18 @@ pub fn manysearch(
     // Load query collection
     let query_collection = load_collection(
         &query_filepath,
-        selection,
+        &selection,
         ReportType::Query,
         allow_failed_sigpaths,
     )?;
 
     // load all query sketches into memory, downsampling on the way
-    let query_sketchlist = query_collection.load_sketches(selection)?;
+    let query_sketchlist = query_collection.load_sketches(&selection)?;
 
     // Against: Load collection, potentially off disk & not into memory.
     let against_collection = load_collection(
         &against_filepath,
-        selection,
+        &selection,
         ReportType::Against,
         allow_failed_sigpaths,
     )?;
diff --git a/src/mastiff_manygather.rs b/src/mastiff_manygather.rs
index 6839d250..4d15f696 100644
--- a/src/mastiff_manygather.rs
+++ b/src/mastiff_manygather.rs
@@ -15,7 +15,7 @@ use crate::utils::{
 pub fn mastiff_manygather(
     queries_file: String,
     index: PathBuf,
-    selection: &Selection,
+    selection: Selection,
     threshold_bp: usize,
     output: Option<String>,
     allow_failed_sigpaths: bool,
@@ -29,7 +29,7 @@ pub fn mastiff_manygather(
 
     let query_collection = load_collection(
         &queries_file,
-        selection,
+        &selection,
         ReportType::Query,
         allow_failed_sigpaths,
     )?;
diff --git a/src/mastiff_manysearch.rs b/src/mastiff_manysearch.rs
index 158dded1..ba0d7559 100644
--- a/src/mastiff_manysearch.rs
+++ b/src/mastiff_manysearch.rs
@@ -18,7 +18,7 @@ use crate::utils::{
 pub fn mastiff_manysearch(
     queries_path: String,
     index: PathBuf,
-    selection: &Selection,
+    selection: Selection,
     minimum_containment: f64,
     output: Option<String>,
     allow_failed_sigpaths: bool,
@@ -35,7 +35,7 @@ pub fn mastiff_manysearch(
     // Load query paths
     let query_collection = load_collection(
         &queries_path,
-        selection,
+        &selection,
         ReportType::Query,
         allow_failed_sigpaths,
     )?;
diff --git a/src/multisearch.rs b/src/multisearch.rs
index cf4bacb8..f668dca0 100644
--- a/src/multisearch.rs
+++ b/src/multisearch.rs
@@ -18,7 +18,7 @@ pub fn multisearch(
     query_filepath: String,
     against_filepath: String,
     threshold: f64,
-    selection: &Selection,
+    selection: Selection,
     allow_failed_sigpaths: bool,
     estimate_ani: bool,
     output: Option<String>,
@@ -26,22 +26,39 @@ pub fn multisearch(
     // Load all queries into memory at once.
     let query_collection = load_collection(
         &query_filepath,
-        selection,
+        &selection,
         ReportType::Query,
         allow_failed_sigpaths,
     )?;
 
-    let queries = query_collection.load_sketches(selection)?;
+    let scaled = match selection.scaled() {
+        Some(s) => s,
+        None => {
+            let scaled = query_collection.max_scaled().expect("no records!?").clone() as u32;
+            eprintln!(
+                "Setting scaled={} based on max scaled in query collection",
+                scaled
+            );
+            scaled
+        }
+    };
+
+    let ksize = selection.ksize().unwrap() as f64;
+
+    let mut new_selection = selection;
+    new_selection.set_scaled(scaled as u32);
+
+    let queries = query_collection.load_sketches(&new_selection)?;
 
     // Load all against sketches into memory at once.
     let against_collection = load_collection(
         &against_filepath,
-        selection,
+        &new_selection,
         ReportType::Against,
         allow_failed_sigpaths,
     )?;
 
-    let against = against_collection.load_sketches(selection)?;
+    let against = against_collection.load_sketches(&new_selection)?;
 
     // set up a multi-producer, single-consumer channel.
     let (send, recv) =
@@ -57,7 +74,6 @@ pub fn multisearch(
     //
 
     let processed_cmp = AtomicUsize::new(0);
-    let ksize = selection.ksize().unwrap() as f64;
 
     let send = against
         .par_iter()
@@ -70,7 +86,11 @@ pub fn multisearch(
                     eprintln!("Processed {} comparisons", i);
                 }
 
-                let overlap = query.minhash.count_common(&against.minhash, false).unwrap() as f64;
+                let overlap = query
+                    .minhash
+                    .count_common(&against.minhash, false)
+                    .expect("cannot compare query and against!?")
+                    as f64;
                 // use downsampled sizes
                 let query_size = query.minhash.size() as f64;
                 let target_size = against.minhash.size() as f64;
diff --git a/src/pairwise.rs b/src/pairwise.rs
index 914c44f3..f3e447f1 100644
--- a/src/pairwise.rs
+++ b/src/pairwise.rs
@@ -16,7 +16,7 @@ use sourmash::signature::SigsTrait;
 pub fn pairwise(
     siglist: String,
     threshold: f64,
-    selection: &Selection,
+    selection: Selection,
     allow_failed_sigpaths: bool,
     estimate_ani: bool,
     write_all: bool,
@@ -25,7 +25,7 @@ pub fn pairwise(
     // Load all sigs into memory at once.
     let collection = load_collection(
         &siglist,
-        selection,
+        &selection,
         ReportType::General,
         allow_failed_sigpaths,
     )?;
@@ -37,7 +37,7 @@ pub fn pairwise(
         )
     }
 
-    let sketches = collection.load_sketches(selection)?;
+    let sketches = collection.load_sketches(&selection)?;
 
     // set up a multi-producer, single-consumer channel.
     let (send, recv) =
diff --git a/src/python/sourmash_plugin_branchwater/__init__.py b/src/python/sourmash_plugin_branchwater/__init__.py
index 116d2072..58b80788 100755
--- a/src/python/sourmash_plugin_branchwater/__init__.py
+++ b/src/python/sourmash_plugin_branchwater/__init__.py
@@ -249,9 +249,9 @@ def __init__(self, p):
         p.add_argument(
             "-s",
             "--scaled",
-            default=1000,
+            default=None,
             type=int,
-            help="scaled factor at which to do comparisons (default: 1000)",
+            help="scaled factor at which to do comparisons (default: determined from query collection)",
         )
         p.add_argument(
             "-m",
@@ -435,9 +435,9 @@ def __init__(self, p):
         p.add_argument(
             "-s",
             "--scaled",
-            default=1000,
+            default=None,
             type=int,
-            help="scaled factor at which to do comparisons",
+            help="scaled factor at which to do comparisons (default: determined from query collection)",
         )
         p.add_argument(
             "-m",
diff --git a/src/python/tests/test_fastmultigather.py b/src/python/tests/test_fastmultigather.py
index a21de63e..522cf17e 100644
--- a/src/python/tests/test_fastmultigather.py
+++ b/src/python/tests/test_fastmultigather.py
@@ -1987,3 +1987,100 @@ def test_create_empty_results(runtmp):
     g_output = runtmp.output("CP001071.1.gather.csv")
     p_output = runtmp.output("CP001071.1.prefetch.csv")
     assert os.path.exists(p_output)
+
+
+def test_simple_against_scaled(runtmp, zip_against):
+    # we shouldn't automatically downsample query
+    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")
+
+    downsampled_sigs = runtmp.output("ds.sig.zip")
+    runtmp.sourmash(
+        "sig",
+        "downsample",
+        "--scaled",
+        "120_000",
+        sig2,
+        sig47,
+        sig63,
+        "-o",
+        downsampled_sigs,
+    )
+
+    query_list = runtmp.output("query.txt")
+    make_file_list(query_list, [query])
+
+    with pytest.raises(utils.SourmashCommandFailed):
+        runtmp.sourmash(
+            "scripts",
+            "fastmultigather",
+            query_list,
+            downsampled_sigs,
+            "-t",
+            "0",
+            in_directory=runtmp.output(""),
+        )
+
+
+def test_simple_query_scaled(runtmp):
+    # test basic execution w/automatic scaled selection based on query
+    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")
+
+    query_list = runtmp.output("query.txt")
+    against_list = runtmp.output("against.txt")
+
+    make_file_list(query_list, [query])
+    make_file_list(against_list, [sig2, sig47, sig63])
+
+    runtmp.sourmash(
+        "scripts",
+        "fastmultigather",
+        query_list,
+        against_list,
+        "-t",
+        "0",
+        in_directory=runtmp.output(""),
+    )
+
+    print(os.listdir(runtmp.output("")))
+
+    g_output = runtmp.output("SRR606249.gather.csv")
+    assert os.path.exists(g_output)
+
+
+def test_simple_query_scaled_indexed(runtmp):
+    # test basic execution w/automatic scaled selection based on query
+    # (on a rocksdb)
+    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")
+
+    query_list = runtmp.output("query.txt")
+    against_list = runtmp.output("against.txt")
+
+    make_file_list(query_list, [query])
+    make_file_list(against_list, [sig2, sig47, sig63])
+    against_list = index_siglist(runtmp, against_list, runtmp.output("against.rocksdb"))
+
+    runtmp.sourmash(
+        "scripts",
+        "fastmultigather",
+        query_list,
+        against_list,
+        "-o",
+        "foo.csv",
+        "-t",
+        "0",
+        in_directory=runtmp.output(""),
+    )
+
+    print(os.listdir(runtmp.output("")))
+
+    g_output = runtmp.output("foo.csv")
+    assert os.path.exists(g_output)
diff --git a/src/python/tests/test_multisearch.py b/src/python/tests/test_multisearch.py
index 43b6715a..ef018a96 100644
--- a/src/python/tests/test_multisearch.py
+++ b/src/python/tests/test_multisearch.py
@@ -1176,3 +1176,48 @@ def test_simple_below_threshold(runtmp):
             assert float(row["match_containment_ani"]) == 1.0
             assert float(row["average_containment_ani"]) == 1.0
             assert float(row["max_containment_ani"]) == 1.0
+
+
+def test_mismatched_scaled_query(runtmp):
+    # test what happens if query scaled is too high
+    query_list = runtmp.output("query.txt")
+    against_list = runtmp.output("against.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")
+
+    query_list = runtmp.output("downsample.sig.zip")
+    runtmp.sourmash(
+        "sig", "downsample", "--scaled=10_000", sig2, sig47, sig63, "-o", query_list
+    )
+    make_file_list(against_list, [sig2, sig47, sig63])
+
+    output = runtmp.output("out.csv")
+
+    runtmp.sourmash("scripts", "multisearch", query_list, against_list, "-o", output)
+    assert os.path.exists(output)
+
+
+def test_mismatched_scaled_against(runtmp):
+    # test what happens if against scaled is too high
+    query_list = runtmp.output("query.txt")
+    against_list = runtmp.output("against.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(query_list, [sig2, sig47, sig63])
+
+    against_list = runtmp.output("downsample.sig.zip")
+    runtmp.sourmash(
+        "sig", "downsample", "--scaled=10_000", sig2, sig47, sig63, "-o", against_list
+    )
+
+    output = runtmp.output("out.csv")
+
+    with pytest.raises(utils.SourmashCommandFailed):
+        runtmp.sourmash(
+            "scripts", "multisearch", query_list, against_list, "-o", output
+        )
diff --git a/src/utils/mod.rs b/src/utils/mod.rs
index d5285820..a29b794e 100644
--- a/src/utils/mod.rs
+++ b/src/utils/mod.rs
@@ -580,6 +580,7 @@ pub fn load_collection(
     match collection {
         Some((coll, n_failed)) => {
             let n_total = coll.len();
+
             let selected = coll.select(selection)?;
             let n_skipped = n_total - selected.len();
             report_on_collection_loading(
@@ -955,7 +956,7 @@ pub fn consume_query_by_gather(
     Ok(())
 }
 
-pub fn build_selection(ksize: u8, scaled: usize, moltype: &str) -> Selection {
+pub fn build_selection(ksize: u8, scaled: Option<usize>, moltype: &str) -> Selection {
     let hash_function = match moltype {
         "DNA" => HashFunctions::Murmur64Dna,
         "protein" => HashFunctions::Murmur64Protein,
@@ -967,11 +968,18 @@ pub fn build_selection(ksize: u8, scaled: usize, moltype: &str) -> Selection {
     //     .map_err(|_| panic!("Unknown molecule type: {}", moltype))
     //     .unwrap();
 
-    Selection::builder()
-        .ksize(ksize.into())
-        .scaled(scaled as u32)
-        .moltype(hash_function)
-        .build()
+    if let Some(scaled) = scaled {
+        Selection::builder()
+            .ksize(ksize.into())
+            .scaled(scaled as u32)
+            .moltype(hash_function)
+            .build()
+    } else {
+        Selection::builder()
+            .ksize(ksize.into())
+            .moltype(hash_function)
+            .build()
+    }
 }
 
 pub fn is_revindex_database(path: &camino::Utf8PathBuf) -> bool {
diff --git a/src/utils/multicollection.rs b/src/utils/multicollection.rs
index 82a351ed..03de24cb 100644
--- a/src/utils/multicollection.rs
+++ b/src/utils/multicollection.rs
@@ -275,6 +275,10 @@ impl MultiCollection {
         val == 0
     }
 
+    pub fn max_scaled(&self) -> Option<&u64> {
+        self.item_iter().map(|(_, _, record)| record.scaled()).max()
+    }
+
     // iterate over tuples
     pub fn item_iter(&self) -> impl Iterator<Item = (&Collection, Idx, &Record)> {
         let s: Vec<_> = self