diff --git a/dorado/cli/aligner.cpp b/dorado/cli/aligner.cpp
index a1637f78..35999ffd 100644
--- a/dorado/cli/aligner.cpp
+++ b/dorado/cli/aligner.cpp
@@ -53,7 +53,14 @@ int aligner(int argc, char* argv[]) {
             .help("maximum number of reads to process (for debugging, 0=unlimited).")
             .default_value(0)
             .scan<'i', int>();
-    parser.visible.add_argument("-v", "--verbose").default_value(false).implicit_value(true);
+    int verbosity = 0;
+    parser.visible.add_argument("-v", "--verbose")
+            .default_value(false)
+            .implicit_value(true)
+            .nargs(0)
+            .action([&](const auto&) { ++verbosity; })
+            .append();
+
     cli::add_minimap2_arguments(parser, Aligner::dflt_options);
 
     try {
@@ -67,7 +74,7 @@ int aligner(int argc, char* argv[]) {
 
     if (parser.visible.get<bool>("--verbose")) {
         mm_verbose = 3;
-        utils::SetDebugLogging();
+        utils::SetVerboseLogging(static_cast<dorado::utils::VerboseLogLevel>(verbosity));
     }
 
     auto index(parser.visible.get<std::string>("index"));
diff --git a/dorado/cli/basecaller.cpp b/dorado/cli/basecaller.cpp
index de4c60f8..55d1ef10 100644
--- a/dorado/cli/basecaller.cpp
+++ b/dorado/cli/basecaller.cpp
@@ -150,7 +150,7 @@ void setup(std::vector<std::string> args,
     if (estimate_poly_a) {
         current_sink_node = pipeline_desc.add_node<PolyACalculator>(
                 {current_sink_node}, std::thread::hardware_concurrency(),
-                PolyACalculator::get_model_type(model_name));
+                is_rna_model(model_config));
     }
     if (!barcode_kits.empty()) {
         current_sink_node = pipeline_desc.add_node<BarcodeClassifierNode>(
@@ -264,7 +264,13 @@ int basecaller(int argc, char* argv[]) {
 
     parser.visible.add_argument("data").help("the data directory or file (POD5/FAST5 format).");
 
-    parser.visible.add_argument("-v", "--verbose").default_value(false).implicit_value(true);
+    int verbosity = 0;
+    parser.visible.add_argument("-v", "--verbose")
+            .default_value(false)
+            .implicit_value(true)
+            .nargs(0)
+            .action([&](const auto&) { ++verbosity; })
+            .append();
 
     parser.visible.add_argument("-x", "--device")
             .help("device string in format \"cuda:0,...,N\", \"cuda:all\", \"metal\", \"cpu\" "
@@ -389,7 +395,7 @@ int basecaller(int argc, char* argv[]) {
     std::vector<std::string> args(argv, argv + argc);
 
     if (parser.visible.get<bool>("--verbose")) {
-        utils::SetDebugLogging();
+        utils::SetVerboseLogging(static_cast<dorado::utils::VerboseLogLevel>(verbosity));
     }
 
     auto model = parser.visible.get<std::string>("model");
diff --git a/dorado/cli/demux.cpp b/dorado/cli/demux.cpp
index 2fd2bd64..f2d00f1a 100644
--- a/dorado/cli/demux.cpp
+++ b/dorado/cli/demux.cpp
@@ -69,7 +69,13 @@ int demuxer(int argc, char* argv[]) {
     parser.add_argument("-l", "--read-ids")
             .help("A file with a newline-delimited list of reads to demux.")
             .default_value(std::string(""));
-    parser.add_argument("-v", "--verbose").default_value(false).implicit_value(true);
+    int verbosity = 0;
+    parser.add_argument("-v", "--verbose")
+            .default_value(false)
+            .implicit_value(true)
+            .nargs(0)
+            .action([&](const auto&) { ++verbosity; })
+            .append();
     parser.add_argument("--emit-fastq")
             .help("Output in fastq format. Default is BAM.")
             .default_value(false)
@@ -99,7 +105,7 @@ int demuxer(int argc, char* argv[]) {
     }
 
     if (parser.get<bool>("--verbose")) {
-        utils::SetDebugLogging();
+        utils::SetVerboseLogging(static_cast<dorado::utils::VerboseLogLevel>(verbosity));
     }
 
     auto reads(parser.get<std::vector<std::string>>("reads"));
diff --git a/dorado/cli/download.cpp b/dorado/cli/download.cpp
index 76464819..4d1aa8db 100644
--- a/dorado/cli/download.cpp
+++ b/dorado/cli/download.cpp
@@ -47,8 +47,6 @@ int download(int argc, char* argv[]) {
 
     argparse::ArgumentParser parser("dorado", DORADO_VERSION, argparse::default_arguments::help);
 
-    parser.add_argument("-v", "--verbose").default_value(false).implicit_value(true);
-
     parser.add_argument("--model").default_value(std::string("all")).help("the model to download");
 
     parser.add_argument("--directory")
@@ -62,6 +60,14 @@ int download(int argc, char* argv[]) {
             .default_value(false)
             .implicit_value(true);
 
+    int verbosity = 0;
+    parser.add_argument("-v", "--verbose")
+            .default_value(false)
+            .implicit_value(true)
+            .nargs(0)
+            .action([&](const auto&) { ++verbosity; })
+            .append();
+
     try {
         parser.parse_args(argc, argv);
     } catch (const std::exception& e) {
@@ -72,7 +78,7 @@ int download(int argc, char* argv[]) {
     }
 
     if (parser.get<bool>("--verbose")) {
-        utils::SetDebugLogging();
+        utils::SetVerboseLogging(static_cast<dorado::utils::VerboseLogLevel>(verbosity));
     }
 
     auto list = parser.get<bool>("--list");
diff --git a/dorado/cli/duplex.cpp b/dorado/cli/duplex.cpp
index 2d376748..67962aa2 100644
--- a/dorado/cli/duplex.cpp
+++ b/dorado/cli/duplex.cpp
@@ -110,7 +110,13 @@ int duplex(int argc, char* argv[]) {
             .help("Path to reference for alignment.")
             .default_value(std::string(""));
 
-    parser.visible.add_argument("-v", "--verbose").default_value(false).implicit_value(true);
+    int verbosity = 0;
+    parser.visible.add_argument("-v", "--verbose")
+            .default_value(false)
+            .implicit_value(true)
+            .nargs(0)
+            .action([&](const auto&) { ++verbosity; })
+            .append();
 
     cli::add_minimap2_arguments(parser, Aligner::dflt_options);
     cli::add_internal_arguments(parser);
@@ -133,7 +139,7 @@ int duplex(int argc, char* argv[]) {
         const bool basespace_duplex = (model.compare("basespace") == 0);
         std::vector<std::string> args(argv, argv + argc);
         if (parser.visible.get<bool>("--verbose")) {
-            utils::SetDebugLogging();
+            utils::SetVerboseLogging(static_cast<dorado::utils::VerboseLogLevel>(verbosity));
         }
         std::map<std::string, std::string> template_complement_map;
         auto read_list = utils::load_read_list(parser.visible.get<std::string>("--read-ids"));
diff --git a/dorado/cli/summary.cpp b/dorado/cli/summary.cpp
index 99816b3c..8da957fb 100644
--- a/dorado/cli/summary.cpp
+++ b/dorado/cli/summary.cpp
@@ -50,7 +50,13 @@ int summary(int argc, char *argv[]) {
     argparse::ArgumentParser parser("dorado", DORADO_VERSION, argparse::default_arguments::help);
     parser.add_argument("reads").help("SAM/BAM file produced by dorado basecaller.");
     parser.add_argument("-s", "--separator").default_value(std::string("\t"));
-    parser.add_argument("-v", "--verbose").default_value(false).implicit_value(true);
+    int verbosity = 0;
+    parser.add_argument("-v", "--verbose")
+            .default_value(false)
+            .implicit_value(true)
+            .nargs(0)
+            .action([&](const auto &) { ++verbosity; })
+            .append();
 
     try {
         parser.parse_args(argc, argv);
@@ -62,7 +68,7 @@ int summary(int argc, char *argv[]) {
     }
 
     if (parser.get<bool>("--verbose")) {
-        utils::SetDebugLogging();
+        utils::SetVerboseLogging(static_cast<dorado::utils::VerboseLogLevel>(verbosity));
     }
 
     std::vector<std::string> header = {
diff --git a/dorado/nn/CRFModelConfig.cpp b/dorado/nn/CRFModelConfig.cpp
index b50fd894..d0f84476 100644
--- a/dorado/nn/CRFModelConfig.cpp
+++ b/dorado/nn/CRFModelConfig.cpp
@@ -9,6 +9,18 @@
 
 namespace dorado {
 
+SampleType get_model_type(const std::string &model_name) {
+    if (model_name.find("rna004") != std::string::npos) {
+        return SampleType::RNA004;
+    } else if (model_name.find("rna002") != std::string::npos) {
+        return SampleType::RNA002;
+    } else if (model_name.find("dna") != std::string::npos) {
+        return SampleType::DNA;
+    } else {
+        throw std::runtime_error("Could not determine model type for " + model_name);
+    }
+}
+
 CRFModelConfig load_crf_model_config(const std::filesystem::path &path) {
     const auto config_toml = toml::parse(path / "config.toml");
 
@@ -96,6 +108,8 @@ CRFModelConfig load_crf_model_config(const std::filesystem::path &path) {
         config.signal_norm_params.quantile_scaling = false;
     }
 
+    config.sample_type = get_model_type(model_name);
+
     return config;
 }
 
diff --git a/dorado/nn/CRFModelConfig.h b/dorado/nn/CRFModelConfig.h
index f01a1444..fb360c19 100644
--- a/dorado/nn/CRFModelConfig.h
+++ b/dorado/nn/CRFModelConfig.h
@@ -15,6 +15,12 @@ struct SignalNormalisationParams {
     bool quantile_scaling = true;
 };
 
+enum SampleType {
+    DNA,
+    RNA002,
+    RNA004,
+};
+
 // Values extracted from config.toml used in construction of the model module.
 struct CRFModelConfig {
     float qscale = 1.0f;
@@ -42,6 +48,8 @@ struct CRFModelConfig {
     // Start position for mean Q-score calculation for
     // short reads.
     int32_t mean_qscore_start_pos = -1;
+
+    SampleType sample_type;
 };
 
 CRFModelConfig load_crf_model_config(const std::filesystem::path& path);
diff --git a/dorado/read_pipeline/Pipelines.cpp b/dorado/read_pipeline/Pipelines.cpp
index 84a1c1ee..8331edaf 100644
--- a/dorado/read_pipeline/Pipelines.cpp
+++ b/dorado/read_pipeline/Pipelines.cpp
@@ -62,7 +62,7 @@ void create_simplex_pipeline(PipelineDescriptor& pipeline_desc,
 
     auto scaler_node =
             pipeline_desc.add_node<ScalerNode>({basecaller_node}, model_config.signal_norm_params,
-                                               is_rna_model(model_config), scaler_node_threads);
+                                               model_config.sample_type, scaler_node_threads);
 
     // if we've been provided a source node, connect it to the start of our pipeline
     if (source_node_handle != PipelineDescriptor::InvalidNodeHandle) {
@@ -130,8 +130,9 @@ void create_stereo_duplex_pipeline(PipelineDescriptor& pipeline_desc,
             {splitter_node}, std::move(runners), adjusted_simplex_overlap, kSimplexBatchTimeoutMS,
             model_name, 1000, "BasecallerNode", true, mean_qscore_start_pos);
 
-    auto scaler_node = pipeline_desc.add_node<ScalerNode>(
-            {basecaller_node}, model_config.signal_norm_params, false, scaler_node_threads);
+    auto scaler_node =
+            pipeline_desc.add_node<ScalerNode>({basecaller_node}, model_config.signal_norm_params,
+                                               SampleType::DNA, scaler_node_threads);
 
     // if we've been provided a source node, connect it to the start of our pipeline
     if (source_node_handle != PipelineDescriptor::InvalidNodeHandle) {
diff --git a/dorado/read_pipeline/PolyACalculator.cpp b/dorado/read_pipeline/PolyACalculator.cpp
index b774bb8c..c3ffb6cf 100644
--- a/dorado/read_pipeline/PolyACalculator.cpp
+++ b/dorado/read_pipeline/PolyACalculator.cpp
@@ -256,57 +256,11 @@ SignalAnchorInfo determine_signal_anchor_and_strand_cdna(const dorado::SimplexRe
     return result;
 }
 
-// Since the adapter in RNA is still DNA, the basecall quality of the adapter is poor because we
-// infer with a model trained on RNA data. So finding a match of the adapter sequence in the RNA sequence
-// doesn't work well. Instead, the raw signal is traversed to find a point
-// where there's a jump in the median signal value, which is indicative of the
-// transition from the DNA adapter to the RNA signal. The polyA will start right
-// at that juncture. This function returns a struct with the strand
-// direction (which is always reverse for dRNA), the signal anchor and the number of bases
-// to omit from the tail length estimation due to any adapter effects.
-SignalAnchorInfo determine_signal_anchor_and_strand_drna(
-        const dorado::SimplexRead& read,
-        dorado::PolyACalculator::ModelType model_type) {
-    static const std::unordered_map<dorado::PolyACalculator::ModelType, int> kOffsetMap = {
-            {dorado::PolyACalculator::ModelType::RNA002, 5000},
-            {dorado::PolyACalculator::ModelType::RNA004, 1000}};
-    static const std::unordered_map<dorado::PolyACalculator::ModelType, int> kMaxSignalPosMap = {
-            {dorado::PolyACalculator::ModelType::RNA002, 10000},
-            {dorado::PolyACalculator::ModelType::RNA004, 5000}};
-
-    const int kWindowSize = 250;
-    const int kStride = 50;
-    const int kOffset = kOffsetMap.at(model_type);
-    const int kMaxSignalPos = kMaxSignalPosMap.at(model_type);
-
-    const float kMinMedianForRNASignal = 0.f;
-    const float kMinMedianDiff = 1.f;
-
-    int bp = -1;
-    int signal_len = read.read_common.get_raw_data_samples();
-    auto sig_fp32 = read.read_common.raw_data.to(torch::kFloat);
-    float last_median = 0.f;
-    for (int i = kOffset; i < std::min(signal_len / 2, kMaxSignalPos); i += kStride) {
-        auto slice = sig_fp32.slice(0, std::max(0, i - kWindowSize / 2),
-                                    std::min(signal_len, i + kWindowSize / 2));
-        float median = slice.median().item<float>();
-        if (median > kMinMedianForRNASignal) {
-            float diff = median - last_median;
-            if (diff > kMinMedianDiff) {
-                bp = i;
-                break;
-            }
-        }
-        last_median = median;
-    }
-
-    spdlog::debug("Approx break point {}", bp);
-
-    if (bp > 0) {
-        return SignalAnchorInfo{false, bp, 0};
-    } else {
-        return SignalAnchorInfo{false, -1, 0};
-    }
+// RNA polyA appears at the beginning of the strand. Since the adapter
+// for RNA has been trimmed off already, the polyA search can begin
+// from the start of the signal.
+SignalAnchorInfo determine_signal_anchor_and_strand_drna(const dorado::SimplexRead& read) {
+    return SignalAnchorInfo{false, 0, 0};
 }
 
 }  // namespace
@@ -330,7 +284,7 @@ void PolyACalculator::worker_thread() {
         // Determine the strand direction, approximate base space anchor for the tail, and whether
         // the final length needs to be adjusted depending on the adapter sequence.
         auto [fwd, signal_anchor, trailing_Ts] =
-                m_is_rna ? determine_signal_anchor_and_strand_drna(*read, m_model_type)
+                m_is_rna ? determine_signal_anchor_and_strand_drna(*read)
                          : determine_signal_anchor_and_strand_cdna(*read);
 
         if (signal_anchor >= 0) {
@@ -358,7 +312,7 @@ void PolyACalculator::worker_thread() {
                 // Update debug stats.
                 total_tail_lengths_called += num_bases;
                 ++num_called;
-                if (spdlog::get_level() == spdlog::level::debug) {
+                if (spdlog::get_level() <= spdlog::level::debug) {
                     std::lock_guard<std::mutex> lock(m_mutex);
                     tail_length_counts[num_bases]++;
                 }
@@ -378,13 +332,8 @@ void PolyACalculator::worker_thread() {
     }
 }
 
-PolyACalculator::PolyACalculator(size_t num_worker_threads,
-                                 PolyACalculator::ModelType model_type,
-                                 size_t max_reads)
-        : MessageSink(max_reads),
-          m_num_worker_threads(num_worker_threads),
-          m_is_rna(model_type == ModelType::RNA004 || model_type == ModelType::RNA002),
-          m_model_type(model_type) {
+PolyACalculator::PolyACalculator(size_t num_worker_threads, bool is_rna, size_t max_reads)
+        : MessageSink(max_reads), m_num_worker_threads(num_worker_threads), m_is_rna(is_rna) {
     start_threads();
 }
 
@@ -410,14 +359,14 @@ void PolyACalculator::terminate_impl() {
 
     // Visualize a distribution of the tail lengths called.
     static bool done = false;
-    if (!done && spdlog::get_level() == spdlog::level::debug) {
+    if (!done && (spdlog::get_level() <= spdlog::level::debug)) {
         int max_val = -1;
         for (auto [k, v] : tail_length_counts) {
             max_val = std::max(v, max_val);
         }
         int factor = std::max(1, 1 + max_val / 100);
         for (auto [k, v] : tail_length_counts) {
-            spdlog::debug("{} : {}", k, std::string(v / factor, '*'));
+            spdlog::debug("{:03d} : {}", k, std::string(v / factor, '*'));
         }
         done = true;
     }
@@ -437,16 +386,4 @@ stats::NamedStats PolyACalculator::sample_stats() const {
     return stats;
 }
 
-PolyACalculator::ModelType PolyACalculator::get_model_type(const std::string& model_name) {
-    if (model_name.find("rna004") != std::string::npos) {
-        return PolyACalculator::ModelType::RNA004;
-    } else if (model_name.find("rna002") != std::string::npos) {
-        return PolyACalculator::ModelType::RNA002;
-    } else if (model_name.find("dna") != std::string::npos) {
-        return PolyACalculator::ModelType::DNA;
-    } else {
-        throw std::runtime_error("Could not determine model type for " + model_name);
-    }
-}
-
 }  // namespace dorado
diff --git a/dorado/read_pipeline/PolyACalculator.h b/dorado/read_pipeline/PolyACalculator.h
index d66a3f60..0431601a 100644
--- a/dorado/read_pipeline/PolyACalculator.h
+++ b/dorado/read_pipeline/PolyACalculator.h
@@ -15,19 +15,12 @@ namespace dorado {
 
 class PolyACalculator : public MessageSink {
 public:
-    enum ModelType {
-        DNA,
-        RNA002,
-        RNA004,
-    };
-
-    PolyACalculator(size_t num_worker_threads, ModelType model_type, size_t max_reads = 1000);
+    PolyACalculator(size_t num_worker_threads, bool is_rna, size_t max_reads = 1000);
     ~PolyACalculator() { terminate_impl(); }
     std::string get_name() const override { return "PolyACalculator"; }
     stats::NamedStats sample_stats() const override;
     void terminate(const FlushOptions& flush_options) override { terminate_impl(); };
     void restart() override;
-    static ModelType get_model_type(const std::string& model_name);
 
 private:
     void start_threads();
@@ -38,7 +31,6 @@ class PolyACalculator : public MessageSink {
     std::vector<std::unique_ptr<std::thread>> m_workers;
     size_t m_num_worker_threads = 0;
     const bool m_is_rna;
-    const ModelType m_model_type;
     std::atomic<size_t> total_tail_lengths_called{0};
     std::atomic<int> num_called{0};
     std::atomic<int> num_not_called{0};
diff --git a/dorado/read_pipeline/ScalerNode.cpp b/dorado/read_pipeline/ScalerNode.cpp
index c8d63cf6..6f6d0ce3 100644
--- a/dorado/read_pipeline/ScalerNode.cpp
+++ b/dorado/read_pipeline/ScalerNode.cpp
@@ -6,10 +6,13 @@
 #include <spdlog/spdlog.h>
 
 #include <algorithm>
+#include <array>
+#include <cassert>
 #include <chrono>
+#include <cstdint>
 #include <utility>
 
-#define EPS 1e-9f
+static constexpr float EPS = 1e-9f;
 
 using namespace std::chrono_literals;
 using Slice = torch::indexing::Slice;
@@ -37,6 +40,53 @@ std::pair<float, float> ScalerNode::med_mad(const torch::Tensor& x) {
     return {med.item<float>(), mad.item<float>()};
 }
 
+// This function returns the approximate position where the DNA adapter
+// in a dRNA read ends. The adapter location is determined by looking
+// at the median signal value over a sliding window on the raw signal.
+// RNA002 and RNA004 have different offsets and thresholds for the
+// sliding window heuristic.
+int determine_rna_adapter_pos(const dorado::SimplexRead& read, dorado::SampleType model_type) {
+    assert(read.read_common.raw_data.dtype() == torch::kInt16);
+    static const std::unordered_map<dorado::SampleType, int> kOffsetMap = {
+            {dorado::SampleType::RNA002, 4000}, {dorado::SampleType::RNA004, 1000}};
+    static const std::unordered_map<dorado::SampleType, int16_t> kAdapterCutoff = {
+            {dorado::SampleType::RNA002, 550}, {dorado::SampleType::RNA004, 700}};
+
+    const int kWindowSize = 250;
+    const int kStride = 50;
+    const int16_t kMedianDiff = 125;
+
+    const int kOffset = kOffsetMap.at(model_type);
+    const int16_t kMinMedianForRNASignal = kAdapterCutoff.at(model_type);
+
+    int signal_len = read.read_common.get_raw_data_samples();
+    const int16_t* signal = static_cast<int16_t*>(read.read_common.raw_data.data_ptr());
+
+    // Check the median value change over 5 windows.
+    std::array<int16_t, 5> medians = {0, 0, 0, 0, 0};
+    int median_pos = 0;
+    int break_point = 0;
+    const int signal_start = kOffsetMap.at(model_type);
+    const int signal_end = static_cast<int>(3 * signal_len / 4);
+    for (int i = signal_start; i < signal_end; i += kStride) {
+        auto slice = torch::from_blob(const_cast<int16_t*>(&signal[i]),
+                                      {static_cast<int>(std::min(kWindowSize, signal_len - i))},
+                                      torch::TensorOptions().dtype(torch::kInt16));
+        int16_t median = slice.median().item<int16_t>();
+        medians[median_pos++ % medians.size()] = median;
+        auto minmax = std::minmax_element(medians.begin(), medians.end());
+        int16_t min_median = *minmax.first;
+        int16_t max_median = *minmax.second;
+        if ((median_pos > medians.size()) && (max_median > kMinMedianForRNASignal) &&
+            (max_median - min_median > kMedianDiff)) {
+            break_point = i;
+            break;
+        }
+    }
+
+    return break_point;
+}
+
 void ScalerNode::worker_thread() {
     torch::InferenceMode inference_mode_guard;
 
@@ -50,6 +100,15 @@ void ScalerNode::worker_thread() {
 
         auto read = std::get<SimplexReadPtr>(std::move(message));
 
+        bool is_rna = (m_model_type == SampleType::RNA002 || m_model_type == SampleType::RNA004);
+        // Trim adapter for RNA first before scaling.
+        int trim_start = 0;
+        if (is_rna) {
+            trim_start = determine_rna_adapter_pos(*read, m_model_type);
+            read->read_common.raw_data =
+                    read->read_common.raw_data.index({Slice(trim_start, torch::indexing::None)});
+        }
+
         assert(read->read_common.raw_data.dtype() == torch::kInt16);
         const auto [shift, scale] = m_scaling_params.quantile_scaling
                                             ? normalisation(read->read_common.raw_data)
@@ -68,20 +127,20 @@ void ScalerNode::worker_thread() {
         read->read_common.shift = read->scaling * (shift + read->offset);
 
         // Don't perform DNA trimming on RNA since it looks too different and we lose useful signal.
-        int trim_start = 0;
-        if (!m_is_rna) {
+        if (!is_rna) {
             // 8000 value may be changed in future. Currently this is found to work well.
             int max_samples =
                     std::min(8000, static_cast<int>(read->read_common.get_raw_data_samples() / 2));
             trim_start = utils::trim(
                     read->read_common.raw_data.index({Slice(torch::indexing::None, max_samples)}));
+            read->read_common.raw_data =
+                    read->read_common.raw_data.index({Slice(trim_start, torch::indexing::None)});
         }
 
-        read->read_common.raw_data =
-                read->read_common.raw_data.index({Slice(trim_start, torch::indexing::None)});
         read->read_common.num_trimmed_samples = trim_start;
 
-        spdlog::debug("{} {} {} {}", read->read_common.read_id, shift, scale, trim_start);
+        spdlog::trace("ScalerNode: {} shift: {} scale: {} trim: {}", read->read_common.read_id,
+                      shift, scale, trim_start);
 
         // Pass the read to the next node
         send_message_to_sink(std::move(read));
@@ -89,13 +148,13 @@ void ScalerNode::worker_thread() {
 }
 
 ScalerNode::ScalerNode(const SignalNormalisationParams& config,
-                       bool is_rna,
+                       SampleType model_type,
                        int num_worker_threads,
                        size_t max_reads)
         : MessageSink(max_reads),
           m_scaling_params(config),
           m_num_worker_threads(num_worker_threads),
-          m_is_rna(is_rna) {
+          m_model_type(model_type) {
     start_threads();
 }
 
diff --git a/dorado/read_pipeline/ScalerNode.h b/dorado/read_pipeline/ScalerNode.h
index fda9654c..743faae4 100644
--- a/dorado/read_pipeline/ScalerNode.h
+++ b/dorado/read_pipeline/ScalerNode.h
@@ -16,7 +16,7 @@ namespace dorado {
 class ScalerNode : public MessageSink {
 public:
     ScalerNode(const SignalNormalisationParams& config,
-               bool is_rna,
+               SampleType model_type,
                int num_worker_threads = 5,
                size_t max_reads = 1000);
     ~ScalerNode() { terminate_impl(); }
@@ -33,7 +33,7 @@ class ScalerNode : public MessageSink {
     std::atomic<int> m_num_worker_threads;
 
     SignalNormalisationParams m_scaling_params;
-    const bool m_is_rna;
+    const SampleType m_model_type;
 
     std::pair<float, float> med_mad(const torch::Tensor& x);
     std::pair<float, float> normalisation(const torch::Tensor& x);
diff --git a/dorado/utils/log_utils.cpp b/dorado/utils/log_utils.cpp
index 88cbf3fc..ba22abeb 100644
--- a/dorado/utils/log_utils.cpp
+++ b/dorado/utils/log_utils.cpp
@@ -73,9 +73,13 @@ void InitLogging() {
     }
 }
 
-void SetDebugLogging() {
+void SetVerboseLogging(VerboseLogLevel level) {
     if (is_safe_to_log()) {
-        spdlog::set_level(spdlog::level::debug);
+        if (level >= VerboseLogLevel::TRACE) {
+            spdlog::set_level(spdlog::level::trace);
+        } else if (level <= VerboseLogLevel::DEBUG) {
+            spdlog::set_level(spdlog::level::debug);
+        }
     }
 }
 
diff --git a/dorado/utils/log_utils.h b/dorado/utils/log_utils.h
index d01b3aae..910fb273 100644
--- a/dorado/utils/log_utils.h
+++ b/dorado/utils/log_utils.h
@@ -5,6 +5,11 @@ namespace dorado::utils {
 // Initialises the default logger to point to stderr.
 void InitLogging();
 
-void SetDebugLogging();
+enum class VerboseLogLevel {
+    DEBUG = 1,
+    TRACE = 2,
+};
+
+void SetVerboseLogging(VerboseLogLevel level);
 
 }  // namespace dorado::utils
diff --git a/tests/NodeSmokeTest.cpp b/tests/NodeSmokeTest.cpp
index 9bb453dc..479955cf 100644
--- a/tests/NodeSmokeTest.cpp
+++ b/tests/NodeSmokeTest.cpp
@@ -3,6 +3,7 @@
 #include "decode/CPUDecoder.h"
 #include "models/models.h"
 #include "nn/CRFModel.h"
+#include "nn/CRFModelConfig.h"
 #include "nn/ModBaseModel.h"
 #include "nn/ModBaseRunner.h"
 #include "nn/ModelRunner.h"
@@ -163,9 +164,10 @@ TempDir download_model(const std::string& model) {
 
 DEFINE_TEST(NodeSmokeTestRead, "ScalerNode") {
     auto pipeline_restart = GENERATE(false, true);
-    auto is_rna = GENERATE(true, false);
+    auto model_type = GENERATE(dorado::SampleType::DNA, dorado::SampleType::RNA002,
+                               dorado::SampleType::RNA004);
     CAPTURE(pipeline_restart);
-    CAPTURE(is_rna);
+    CAPTURE(model_type);
 
     set_pipeline_restart(pipeline_restart);
 
@@ -179,7 +181,7 @@ DEFINE_TEST(NodeSmokeTestRead, "ScalerNode") {
     config.quantile_b = 0.9;
     config.shift_multiplier = 0.51;
     config.scale_multiplier = 0.53;
-    run_smoke_test<dorado::ScalerNode>(config, is_rna, 2);
+    run_smoke_test<dorado::ScalerNode>(config, model_type, 2);
 }
 
 DEFINE_TEST(NodeSmokeTestRead, "BasecallerNode") {
@@ -370,8 +372,7 @@ TEST_CASE("BarcodeClassifierNode: test simple pipeline with fastq and sam files"
 
 DEFINE_TEST(NodeSmokeTestRead, "PolyACalculator") {
     auto pipeline_restart = GENERATE(false, true);
-    auto is_rna = GENERATE(dorado::PolyACalculator::ModelType::DNA,
-                           dorado::PolyACalculator::ModelType::RNA004);
+    auto is_rna = GENERATE(false, true);
     CAPTURE(pipeline_restart);
     CAPTURE(is_rna);
 
diff --git a/tests/PolyACalculatorTest.cpp b/tests/PolyACalculatorTest.cpp
index 218f55e3..f8c9ac7a 100644
--- a/tests/PolyACalculatorTest.cpp
+++ b/tests/PolyACalculatorTest.cpp
@@ -5,6 +5,7 @@
 #include "utils/sequence_utils.h"
 
 #include <catch2/catch.hpp>
+#include <spdlog/spdlog.h>
 #include <torch/torch.h>
 
 #include <cstdint>
@@ -21,20 +22,18 @@ using namespace dorado;
 struct TestCase {
     int estimated_bases = 0;
     std::string test_dir;
-    PolyACalculator::ModelType model_type;
+    bool is_rna;
 };
 
 TEST_CASE("PolyACalculator: Test polyT tail estimation", TEST_GROUP) {
-    auto [gt, data, model_type] =
-            GENERATE(TestCase{92, "poly_a/r9_rev_cdna", PolyACalculator::ModelType::DNA},
-                     TestCase{31, "poly_a/r10_fwd_cdna", PolyACalculator::ModelType::DNA},
-                     TestCase{29, "poly_a/rna002", PolyACalculator::ModelType::RNA002},
-                     TestCase{64, "poly_a/rna004", PolyACalculator::ModelType::RNA004});
+    auto [gt, data, is_rna] = GENERATE(
+            TestCase{92, "poly_a/r9_rev_cdna", false}, TestCase{31, "poly_a/r10_fwd_cdna", false},
+            TestCase{28, "poly_a/rna002", true}, TestCase{67, "poly_a/rna004", true});
 
     dorado::PipelineDescriptor pipeline_desc;
     std::vector<dorado::Message> messages;
     auto sink = pipeline_desc.add_node<MessageSinkToVector>({}, 100, messages);
-    auto estimator = pipeline_desc.add_node<PolyACalculator>({sink}, 2, model_type);
+    auto estimator = pipeline_desc.add_node<PolyACalculator>({sink}, 2, is_rna);
 
     auto pipeline = dorado::Pipeline::create(std::move(pipeline_desc));
 
diff --git a/tests/data/poly_a/rna002/moves.bin b/tests/data/poly_a/rna002/moves.bin
index 22493b27..6f741d44 100644
Binary files a/tests/data/poly_a/rna002/moves.bin and b/tests/data/poly_a/rna002/moves.bin differ
diff --git a/tests/data/poly_a/rna002/seq.txt b/tests/data/poly_a/rna002/seq.txt
index bc7cc35d..8031d19e 100644
--- a/tests/data/poly_a/rna002/seq.txt
+++ b/tests/data/poly_a/rna002/seq.txt
@@ -1 +1 @@
-GGTATCCATGGTTACGACCTGATTTCGAAAAACTGGTAGCCAGCTATCAGGCCGGAAGAGGTCACCATGCGCTACTCAACTTCAGGCGTTACCGGGCATGGGCGATGATGCTTTAATCTACGCCCTGAGCCGTTATTTACTCTGCCAACAACCGCAGGGCCTTTCAAAGTTGCGGTCACTGTCGTGGATGTCAGTTGATGCAGGCTGGCACGCATCCCGATTACTACACCGGCCCGAAAAGGAAAAAATACGCTGGGCGTTGATGCGGTACGTGAGGTCACCGAAAAAGCTGAATGAGCACGCACGCTTAGGTGGTGCGAAAGTCGTTTGGGTAACCGATGCTGCCTTACTATCGACGCCGCGGCTAACGCATTGCTGAAAACGCTCGAAGAGCCAGCAGAAACTGGTTTTCCTGGCTACCCGCGAGCCTGAACGTTTACTGGCAACATTACGTAGTCGTTGTCGGTTACCTTTTGCGCCGCCGGAACAGTACGCCGTGACCTGGCTTTCACGCGAAGTGACAATGTCACAGGATGCATTACTTCTGCCGCATTGCGCTTAAGCGCCGGTACGTCTGGCGCGGCACTGGCGTTGTTTCAGGGAGATAACTGGCAGGCTCGTGAAACATTTGTGTCAGGCGTTGGCTAGCGTGCCATCGGGCGACTGGTATTCGCTGCTGTGGCCCTTAATCATGAACAAGCTCCGGCGCGTTTACACTGGCTGGCAACGTTGCTGATGGATGCGCTAAAACGCCATTATGGTGCTGCGCAGGTGACCAATGTTGATGTGCCGGGCCTGTACGTCGAACTGGCAAACCATCTTTCTCCCTCGCGCCTGCAGGCTATACTGGGGGATGTTTTGCCACATTCGTGAACAGTTAATGTCTGTTACAGGCATCAACCGCGAGCTTTTCATCACCGATCTTTTGCGTTGAGCATTACCTGCATGGGCGTTGTGCTACCAGCTTCCATCTTGGCTGCAAAAAAAAAAATTCCTCCTCCTCTACTCCTATCATCCATCATCATCCCATCATCCATCATCCTCTTATTCC
\ No newline at end of file
+GGTATCCATGGTTACGACCTGATTTCGAAAAACTGGTAGCCAGCTATCAGGCCGGAAGAGGTCACCATGCGCTACTCAACTTCAGGCGTTACCGGGCATGGGCGATGATGCTTTAATCTACGCCCTGAGCCGTTATTTACTCTGCCAACAACCGCAGGGCCTTTCAAAGTTGCGGTCACTGTCGTGGATGTCAGTTGATGCAGGCTGGCACGCATCCCGATTACTACACCCTGACCCGAAAAGGAAAAAATACGCTGGGCGTTGATGCGGTACGTGAGGTCACCGAAAAAGCTGAATGAGCACGCACGCTTAGGTGGTGCGAAAGTCGTTTGGGTAACCGATGCTGCCTTACTATCGACGCCGCGGCTAACGCATTGCTGAAAACGCTCGAAGAGCCAGCAGAAACTGGTTTTTCCTGGCTACCCGCGAGCCTGAACGTTTACTGGCAACATTACGTAGTCGTTGTCGGTTACCTTCTGCGCCGCCGCCGGAACAGTACGCCGTGACCTGGCTTTCACGCGAAGTGACAATGTCACAGGATGCATTACTTCTGCCGCATTGCGCTTAAGCGCCGGTTTTTTGGCGCGGCACTGGCGTTGTTTCAGGGAGATAACTGGCAGGCTCGTGAAACATTGTGCGGCAGGCGTTGGCTAGCGTGCCATCGGGCGACTGGTATTCGCCGTTAGCGGCCCTTAATCATGAACAAGCTCCGGCGCGTTTACACTGGCTGGCAACGTTGCTGATGGATGCGCTAAAACGCCATTATGGTGCTGCGCAGGGGTGACCAATGTTGATGTGCCGGGCCTGTACGTCGAACTGGCAAACCATCTTTCTCCCTCGCGCCTGCAGGCTATACTGGGGGATGTTTTGCCACATTCGTGAACAGTTAATGTCTGTTACAGGCATCAACCGCGAGCTTCATCACCGATTTTGCGTTGAGCATTACCTGCATGGGCGTTGTGCTACCGGTTCCTCATCTTTAAGCTGCAAAAAAAAAATTC
\ No newline at end of file
diff --git a/tests/data/poly_a/rna002/signal.tensor b/tests/data/poly_a/rna002/signal.tensor
index 9616f0cb..038c2a64 100644
Binary files a/tests/data/poly_a/rna002/signal.tensor and b/tests/data/poly_a/rna002/signal.tensor differ
diff --git a/tests/data/poly_a/rna004/moves.bin b/tests/data/poly_a/rna004/moves.bin
index 4c5bcbf6..42466a66 100644
Binary files a/tests/data/poly_a/rna004/moves.bin and b/tests/data/poly_a/rna004/moves.bin differ
diff --git a/tests/data/poly_a/rna004/seq.txt b/tests/data/poly_a/rna004/seq.txt
index de95ddc4..fe28fdc2 100644
--- a/tests/data/poly_a/rna004/seq.txt
+++ b/tests/data/poly_a/rna004/seq.txt
@@ -1 +1 @@
-AAATGTCTTTGCTTACATCATCACGTTTATCGGCGCTTTAGCGCCATCCAGGCTGCCTGGGCGGTTGATTATCCGCTCAACCGGAAGCCGACTGGTTGGGCAAAATCAAACGTATACGGTGCAAGAAGAGGATAAAAACAAGGCATTGCCCGACGTTTTGATACTGCGGCAATGTTGATCTGAAGCCAATAACACTATCGCCCCGGTGCCAAAACCTGGTACGACGATAACTATTCCTTCACAACTGTATTACCTGATGCACCGCGTACAGGGGATTATCGTTAACCTTGCAGAGCTGCGCCTTTATTATTATCCGCCGGGAGAAAATATTGTGCAGGTCTATCCAATAGGTATTGATTGCAGGGGCTGGAAACGCCGGTGATGGAAACGCGTGTTGGGCAGAAAATCCCTAACCCAACCTGGACGCCTACGGCAGGCATTCGTCAGCGCTGGAGCGTGGCATTAAATTACCGCCAGTCGTTCCTGCCGGACCAAATAACCCGCTAGGACGTTACGCACTGCGCCTCGCGCATGGTAATGGCGAAATACCTTCATCATGGTATCCAGTGCGCCGGACAGCGTCGGTTTGCGCGTCAGTTCAGGGTGTATTCGCATGAATGTCCGGATATTAAAGCCTTGTTCTCCAGCGTGCGGACGGGAACGCCGGTGAAAGTGATCAACGAACCGGTGAAATATTCCGTGAGCCTGCTCAGGATGCGTTATGTTGAAGTACATCGACACTATCGGCAGAAGAACAGCAGAACGTTCAGACAATGCCACACACTGCCAGCAGGCTTTACGCAATTTAAAGACAATAAGGCTGTAGATCAGAAGTTAGTCGATAAAGCGTTGTATCGTCGGGCAGGGTATCCGGTTTCGGTGAGCAGTGGAGCAACTCCCGCAGCCAGCTAATGCGCCTTCAGTAGAGTCAGCGCAGAATGGTGAACCAGAGCAAGGAATATGTTACGCGTGACGCAGTAGGCTGCAAAAAAAAACGATCCCACCCCCATCTACCCACCAATTTATTCCATATCAACCTGCCCCACATCCCTAACTCC
\ No newline at end of file
+AAATGTCTTTGCTTACATCATCACGTTTATCGGCGCTTTTAGCGCCATCCAGGCTGCCTGGGCGGTTGATTATCCGCTCAACCGGAAGCCGACTGGTTGGGCAAAATCAAACGTATACGGTGCAAGAAGGGGATAAAAACAAGGCATTGCCCGACGTTTTGATACTGCGGCAATGTTGATCTGAAGCCAATAACACTATCGCCCCGGTGCCAAAACCTGGTACGACGATAACTATTCCTTCCAACTGTATTACCTGATGCACCGCGTACAGGGGATTATCGTTAACCTTGCAGAGCTGCGCCTTTATTATTATCCGCCGGGAGAAAATATTGTGCAGGTCTATCCAATAGGTATTGATTGCAGGGGCTGGAAACGCCGGTGATGGAAACGCGTGTTGGGCAGAAAATCCCTAACCCAACCTGGACGCCTACGGCAGGCATTCGTCAGCGCTGGAGCGTGGCATTAAATTACCGCCAGTCGTTCCTGCCGGACCAAATAACCCGCTAGGACGTTACGCACTGCGCCTCGCGCATGGTAATGGCGAAATACCTTCATCATGGTATCCAGTGCGCCGGACAGCGTCGGTTTGCGCGTCAGTTCAGGGTGTATTCGCATGAATGTCCGGATATTAAAGCCTTGTTCTCCAGCGTGCGGACGGGAACGCCGGTGAAAGTGATCAACGAACCGGTGAAATATTCCGCGGAGCCTAACGGGATGCGTTATGTTGAAGTACATCGACCACTATCGGCAGAAGAACAGCAGAACGTTCAGACAATGCCACACACTGCCAGCAGGCTTTACGCAATTTAAAGACAATAAGGCTGTAGATCAGAAGTTAGTCGATAAAGCGTTGTATCGTCGGGCAGGGTATCCGGTTTCGGTGAGCAGTGGAGCAACTCCCGCAGCCAGCAATGCGCCTTCAGTAGAGTCAGCGCAGAATGGTGAACCAGAGCAAGGAATATGTTACGCGTGACGCAGTAGGCTGCAAAAAAAAAAAAA
\ No newline at end of file
diff --git a/tests/data/poly_a/rna004/signal.tensor b/tests/data/poly_a/rna004/signal.tensor
index 370d2533..a93d417c 100644
Binary files a/tests/data/poly_a/rna004/signal.tensor and b/tests/data/poly_a/rna004/signal.tensor differ