diff --git a/containers/azimuth/context/main.py b/containers/azimuth/context/main.py
index df51afd..e3a67f0 100644
--- a/containers/azimuth/context/main.py
+++ b/containers/azimuth/context/main.py
@@ -87,6 +87,11 @@ def create_clean_matrix(
         clean_obs = pandas.DataFrame(index=temp_index)
         clean_matrix = matrix.copy()
         clean_matrix.obs = clean_obs
+        clean_matrix.obsm = None
+        clean_matrix.obsp = None
+        clean_matrix.varm = None
+        clean_matrix.varp = None
+        clean_matrix.uns = {}
 
         return clean_matrix
 
diff --git a/containers/azimuth/context/run_azimuth.R b/containers/azimuth/context/run_azimuth.R
index 5d247c3..ce02453 100644
--- a/containers/azimuth/context/run_azimuth.R
+++ b/containers/azimuth/context/run_azimuth.R
@@ -9,7 +9,7 @@ matrix_path <- args[1]
 reference <- args[2]
 
 # Annotate
-options(timeout=60 * 60)
+options(timeout=10 * 60)
 output_data <- RunAzimuth(matrix_path, reference=reference)
 
 # Save and convert to h5ad