diff --git a/src/xfel_calibrate/calibrate.py b/src/xfel_calibrate/calibrate.py
index 7e9fbd58fdead4823223c6f24f43a90dcde39a5c..e83c60a41de3796751e0b7fd7873cfd650f1468e 100755
--- a/src/xfel_calibrate/calibrate.py
+++ b/src/xfel_calibrate/calibrate.py
@@ -644,7 +644,7 @@ def run_finalize(fmt_args, temp_path, job_list, sequential=False):
         finalize_script,
     ]
 
-    output = check_output(cmd).decode('utf8')
+    output = check_output(cmd, input=b'').decode('utf8')
     jobid = None
     if not sequential:
         jobid = output.partition(';')[0].strip()
diff --git a/src/xfel_calibrate/finalize.py b/src/xfel_calibrate/finalize.py
index 4fc25b57ddf2d2c42d1c15472f090acc76e91e24..3683063011ea05753aad60c7cd893c969c502831 100644
--- a/src/xfel_calibrate/finalize.py
+++ b/src/xfel_calibrate/finalize.py
@@ -240,7 +240,7 @@ def make_report(run_path: Path, tmp_path: Path, project: str,
                     "--ext-intersphinx",
                     "--ext-mathjax",
                     "--makefile",
-                    "--no-batchfile", run_path], input=b'')
+                    "--no-batchfile", run_path])
 
     except CalledProcessError:
         raise Exception("Failed to run sphinx-quickstart. Is sphinx installed?"
@@ -322,7 +322,7 @@ def make_report(run_path: Path, tmp_path: Path, project: str,
     chdir(run_path)
     try:
         check_call(["make", f"SPHINXBUILD={sys.executable} -m sphinx",
-                    "latexpdf"], input=b'')
+                    "latexpdf"])
 
     except CalledProcessError:
         print("Failed to make pdf documentation")