diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9e3f8edef84674761ddef9f394378109b39971ab..dc27ec89cc89984743e07e42bb6409461954277b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -42,12 +42,13 @@ stages:
       - echo "packages dir - " $PACKAGES_DIR
       - echo "full-fat run date - " $FULL_FAT_RUN_DATE
       - echo "custom full-fat run date - " $CUSTOM_RUN_DATE
+      - echo "output dir - " $OUTPUT_DIR
       - echo "pythonpath - " $PYTHONPATH
 
       - python3 -V  # Print out python version for debugging
       - pip install coverage
       - mkdir $PACKAGES_DIR
-      - mkdir $OUTPUT_DIR
+      - mkdir -p $OUTPUT_DIR
       - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-source-generation.git" $PACKAGES_DIR/source_gen
       - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews_plotting.git" $PACKAGES_DIR/plotting
       - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/flagdir.git" $PACKAGES_DIR/flagdir