diff --git a/cakes-results/src/genomic/read_silva.rs b/cakes-results/src/genomic/read_silva.rs
index 1500d9494..a3dbbf774 100644
--- a/cakes-results/src/genomic/read_silva.rs
+++ b/cakes-results/src/genomic/read_silva.rs
@@ -51,34 +51,19 @@ pub fn silva_to_dataset(
         .to_str()
         .ok_or_else(|| format!("Could not convert file stem to string for {unaligned_path:?}"))?;
 
-    // Open the file and read the lines.
+    // Open the unaligned sequences file and read the lines.
     let file = File::open(unaligned_path)
         .map_err(|e| format!("Could not open file {unaligned_path:?}: {e}"))?;
     let reader = BufReader::new(file);
-    let lines = reader
+    let sequences = reader
         .lines()
         .map(|line| line.map_err(|e| format!("Could not read line: {e}")))
         .collect::<Result<Vec<_>, _>>()?;
-
-    // shuffle the lines and keep track of the original indices.
-    let mut lines = lines.into_iter().enumerate().collect::<Vec<_>>();
-    lines.shuffle(&mut rand::thread_rng());
-
-    // Collect the first 1000 lines for the query set. The remaining lines are
-    // for the training set.
-    let (train_indices, train_sequences): (Vec<_>, Vec<_>) =
-        lines.split_off(1000).into_iter().unzip();
-    let train = VecDataset::new(
-        format!("{stem}-train"),
-        train_sequences,
-        metric,
-        is_expensive,
+    info!(
+        "Read {} sequences from {unaligned_path:?}.",
+        sequences.len()
     );
 
-    // Collect the lines for the query set.
-    let (query_indices, queries): (Vec<_>, Vec<_>) = lines.into_iter().unzip();
-    let queries = VecDataset::new(format!("{stem}-queries"), queries, metric, is_expensive);
-
     // Read the headers file.
     let file = File::open(headers_path)
         .map_err(|e| format!("Could not open file {headers_path:?}: {e}"))?;
@@ -89,34 +74,38 @@ pub fn silva_to_dataset(
         .collect::<Result<Vec<_>, _>>()?;
     info!("Read {} headers from {headers_path:?}.", headers.len());
 
-    // Split the headers into the training and query sets.
-    let (query_headers, train_headers) = headers
-        .into_iter()
-        .enumerate()
-        .partition::<Vec<_>, _>(|(i, _)| query_indices.contains(i));
+    // join the lines and headers into a single vector of (line, header) pairs.
+    let mut sequences = sequences.into_iter().zip(headers).collect::<Vec<_>>();
+    sequences.shuffle(&mut thread_rng());
+    info!("Shuffled sequences and headers.");
 
-    let train_headers = train_headers
-        .into_iter()
-        .filter(|(i, _)| train_indices.contains(i))
-        .map(|(_, h)| h)
-        .collect::<Vec<_>>();
-    let train_headers = VecDataset::new(
-        format!("{stem}-train-headers"),
-        train_headers,
+    // Split the lines into the training and query sets.
+    let queries = sequences.split_off(1000);
+    let (queries, query_headers): (Vec<_>, Vec<_>) = queries.into_iter().unzip();
+    let queries = VecDataset::new(format!("{stem}-queries"), queries, metric, is_expensive);
+    let query_headers = VecDataset::new(
+        format!("{stem}-query-headers"),
+        query_headers,
         metric,
         is_expensive,
     );
+    info!(
+        "Using {} sequences for queries.",
+        query_headers.cardinality()
+    );
 
-    let query_headers = query_headers
-        .into_iter()
-        .map(|(_, h)| h)
-        .collect::<Vec<_>>();
-    let query_headers = VecDataset::new(
-        format!("{stem}-query-headers"),
-        query_headers,
+    let (train, train_headers): (Vec<_>, Vec<_>) = sequences.into_iter().unzip();
+    let train = VecDataset::new(format!("{stem}-train"), train, metric, is_expensive);
+    let train_headers = VecDataset::new(
+        format!("{stem}-train-headers"),
+        train_headers,
         metric,
         is_expensive,
     );
+    info!(
+        "Using {} sequences for training.",
+        train_headers.cardinality()
+    );
 
     assert_eq!(train.cardinality(), train_headers.cardinality());
     assert_eq!(queries.cardinality(), query_headers.cardinality());