diff --git a/.github/bot-pr-base.sh b/.github/bot-pr-base.sh
index b261bf74324..67f42e91bd0 100644
--- a/.github/bot-pr-base.sh
+++ b/.github/bot-pr-base.sh
@@ -66,7 +66,7 @@ bot_get_all_changed_files() {
   while true; do
     # this api allows 100 items per page
     # github action uses `bash -e`. The last empty page will leads jq error, use `|| :` to ignore the error.
-    local pr_page_files=$(api_get "$pr_url/files?&per_page=100&page=${page}" | jq -er '.[] | .filename' || :)
+    local pr_page_files=$(api_get "$pr_url/files?&per_page=100&page=${page}" | jq -er '.[] | select(.status != "removed") | .filename' || :)
     if [ "${pr_page_files}" = "" ]; then
       break
     fi
diff --git a/.github/bot-pr-format-base.sh b/.github/bot-pr-format-base.sh
index c4171aac779..6821306322c 100644
--- a/.github/bot-pr-format-base.sh
+++ b/.github/bot-pr-format-base.sh
@@ -34,7 +34,7 @@ cp /tmp/format_header.sh dev_tools/scripts/
 cp /tmp/update_ginkgo_header.sh dev_tools/scripts/
 
 # format files
-CLANG_FORMAT=clang-format-8
+CLANG_FORMAT=clang-format-9
 dev_tools/scripts/add_license.sh
 dev_tools/scripts/update_ginkgo_header.sh
 for f in $(echo "$TO_FORMAT" | grep -E $FORMAT_HEADER_REGEX); do dev_tools/scripts/format_header.sh "$f"; done