diff --git a/pyproject.toml b/pyproject.toml
index 7b895e3..9d639ef 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "maxgcp"
-version = "0.1.2"
+version = "0.1.3"
 description = "Optimized phenotype definitions boost GWAS power"
 authors = [
     {name = "zietzm", email = "michael.zietz@gmail.com"}
diff --git a/src/maxgcp/cli.py b/src/maxgcp/cli.py
index 7333455..ff879d8 100644
--- a/src/maxgcp/cli.py
+++ b/src/maxgcp/cli.py
@@ -592,6 +592,9 @@ def run_command(
             maxgcp_weights_path.rename(
                 output_file.parent.joinpath("maxgcp_weights.tsv")
             )
+            # Create empty files to avoid errors when cleaning up
+            covariance_path.touch()
+            maxgcp_weights_path.touch()
         else:
             logger.info("Cleaning up intermediate files")
     logger.info("Done")