diff --git a/casanovo/casanovo.py b/casanovo/casanovo.py
index d146d5f5..95b3a183 100644
--- a/casanovo/casanovo.py
+++ b/casanovo/casanovo.py
@@ -523,7 +523,7 @@ def _setup_output(
         be resolved to the current working directory.
     output_root : str | None
         The base name for the output files. If `None` the output root name will
-        be resolved to casanovo_<current data and time>
+        be resolved to casanovo_<current date and time>
     overwrite: bool
         Whether to overwrite log file if it already exists in the output
         directory.
@@ -544,10 +544,12 @@ def _setup_output(
     if output_dir is None:
         output_path = Path.cwd()
     else:
-        output_path = Path(output_dir)
+        output_path = Path(output_dir).expanduser().resolve()
         if not output_path.is_dir():
-            raise FileNotFoundError(
-                f"Target output directory {output_dir} does not exists."
+            output_path.mkdir(parents=True)
+            warnings.warn(
+                f"Target output directory {output_dir} does not exists, "
+                "so it will be created."
             )
 
     if not overwrite:
diff --git a/casanovo/denovo/model_runner.py b/casanovo/denovo/model_runner.py
index adc4c8cc..73d1da77 100644
--- a/casanovo/denovo/model_runner.py
+++ b/casanovo/denovo/model_runner.py
@@ -72,7 +72,7 @@ def __init__(
 
         if output_dir is None:
             self.callbacks = []
-            warnings.warn(
+            logger.warning(
                 "Checkpoint directory not set in ModelRunner, "
                 "no checkpoint files will be saved."
             )
diff --git a/tests/unit_tests/test_unit.py b/tests/unit_tests/test_unit.py
index f221d502..9ad8490d 100644
--- a/tests/unit_tests/test_unit.py
+++ b/tests/unit_tests/test_unit.py
@@ -7,6 +7,7 @@
 import os
 import pathlib
 import platform
+import re
 import requests
 import shutil
 import tempfile
@@ -944,3 +945,22 @@ def test_check_dir(tmp_path):
 
     utils.check_dir_file_exists(tmp_path, [dne_pattern])
     utils.check_dir_file_exists(tmp_path, dne_pattern)
+
+
+def test_setup_output(tmp_path, monkeypatch):
+    with monkeypatch.context() as mnk:
+        mnk.setattr(pathlib.Path, "cwd", lambda: tmp_path)
+        output_path, output_root = casanovo._setup_output(
+            None, None, False, "info"
+        )
+        assert output_path.resolve() == tmp_path.resolve()
+        assert re.fullmatch(r"casanovo_\d+", output_root) is not None
+
+        target_path = tmp_path / "foo"
+        with pytest.warns(UserWarning):
+            output_path, output_root = casanovo._setup_output(
+                str(target_path), "bar", False, "info"
+            )
+
+        assert output_path.resolve() == target_path.resolve()
+        assert output_root == "bar"