diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5382cbf021d603bbd20cde9c37e995bf5773d1de..14863a6cff98c3cf580edace3dcf3e7354803be5 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -30,7 +30,8 @@ before_script:
   - cd phasexmlparser
   - pip install .
   - cd ../
-  - if [[ ! -d 'phasexmlcreator' ]]; then git clone https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/ssimpleapps/phasexmlcreator.git; fi
+  - if [[ -d 'phasexmlcreator' ]]; then rm -r phasexmlcraetor; fi
+  - git clone https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/ssimpleapps/phasexmlcreator.git
   - cd phasexmlcreator
   - pip install .
   - cd ../
diff --git a/phasecalculator/runners/phasetransferrunner.py b/phasecalculator/runners/phasetransferrunner.py
index e7f48cbf28de06c275a7abb7824efb2127249aca..673310b769cb617cebc5857c187c34a5d42630de 100755
--- a/phasecalculator/runners/phasetransferrunner.py
+++ b/phasecalculator/runners/phasetransferrunner.py
@@ -165,7 +165,7 @@ def run_calculation(arg_list):
         result of system call.
 
     """
-    return subprocess.run(arg_list)
+    return subprocess.run(arg_list,capture_output=True)
 
 
 def generate_vle_calc_args(jar_path, phase_filename, output_filename, **kwargs):