diff --git a/.ci/setup.sh b/.ci/setup.sh
index 78637fad2056..a8aafecbdfea 100755
--- a/.ci/setup.sh
+++ b/.ci/setup.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-echo 53
+echo 54
 
 
 ARCH=$(uname -m)
diff --git a/.github/workflows/cuda.yml b/.github/workflows/cuda.yml
index 864512fcf825..2a645a03b1d1 100644
--- a/.github/workflows/cuda.yml
+++ b/.github/workflows/cuda.yml
@@ -63,7 +63,7 @@ jobs:
           nvidia-smi
 
           # build and test
-          rm -rf $GITHUB_WORKSPACE
+          rm -rf $GITHUB_WORKSPACE/LightGBM
           mkdir -p $GITHUB_WORKSPACE/.ci
           curl --output $GITHUB_WORKSPACE/.ci/setup.sh "https://raw.githubusercontent.com/microsoft/LightGBM/refs/heads/ci/test/.ci/setup.sh"
           chmod +x $GITHUB_WORKSPACE/.ci/setup.sh