diff --git a/src/toil/jobStores/fileJobStore.py b/src/toil/jobStores/fileJobStore.py
index 71729ddd05..e945b6db5b 100644
--- a/src/toil/jobStores/fileJobStore.py
+++ b/src/toil/jobStores/fileJobStore.py
@@ -499,7 +499,7 @@ def update_file(self, file_id, local_path):
 
         atomic_copy(local_path, jobStoreFilePath)
 
-    def read_file(self, file_id, local_path, symlink=False):
+    def read_file(self, file_id: str, local_path: str, symlink: bool = False) -> None:
         self._check_job_store_file_id(file_id)
         jobStoreFilePath = self._get_file_path_from_id(file_id)
         localDirPath = os.path.dirname(local_path)
diff --git a/src/toil/utils/toilClean.py b/src/toil/utils/toilClean.py
index e9a019ea21..69392182aa 100644
--- a/src/toil/utils/toilClean.py
+++ b/src/toil/utils/toilClean.py
@@ -22,9 +22,9 @@
 
 
 def main() -> None:
-    parser = parser_with_common_options(jobstore_option=True)
+    parser = parser_with_common_options(jobstore_option=True, prog="toil clean")
 
-    options = parser.parse_args(prog="toil clean")
+    options = parser.parse_args()
     set_logging_from_options(options)
     try:
         jobstore = Toil.getJobStore(options.jobStore)
diff --git a/src/toil/utils/toilDebugFile.py b/src/toil/utils/toilDebugFile.py
index 62145d8b17..05098f544f 100644
--- a/src/toil/utils/toilDebugFile.py
+++ b/src/toil/utils/toilDebugFile.py
@@ -15,6 +15,7 @@
 import argparse
 import logging
 import os.path
+import sys
 from typing import Optional
 
 from toil.common import Config, Toil, parser_with_common_options
@@ -116,33 +117,33 @@ def main() -> None:
     if options.fetch:
         # Copy only the listed files locally
 
-        if not isinstance(jobStore, FileJobStore):
+        if isinstance(jobStore, FileJobStore):
+            logger.debug("Fetching local files: %s", options.fetch)
+            fetchJobStoreFiles(jobStore=jobStore, options=options)
+        else:
             logger.critical("Can only fetch by name or glob from file-based job stores")
             sys.exit(1)
 
-        logger.debug("Fetching local files: %s", options.fetch)
-        fetchJobStoreFiles(jobStore=jobStore, options=options)
-
     elif options.fetchEntireJobStore:
         # Copy all jobStore files locally
 
-        if not isinstance(jobStore, FileJobStore):
+        if isinstance(jobStore, FileJobStore):
+            logger.debug("Fetching all local files.")
+            options.fetch = "*"
+            fetchJobStoreFiles(jobStore=jobStore, options=options)
+        else:
             logger.critical("Can only fetch by name or glob from file-based job stores")
             sys.exit(1)
 
-        logger.debug("Fetching all local files.")
-        options.fetch = "*"
-        fetchJobStoreFiles(jobStore=jobStore, options=options)
-
     if options.listFilesInJobStore:
         # Log filenames and create a file containing these names in cwd
 
-        if not isinstance(jobStore, FileJobStore):
+        if isinstance(jobStore, FileJobStore):
+            printContentsOfJobStore(job_store=jobStore)
+        else:
             logger.critical("Can only list files from file-based job stores")
             sys.exit(1)
 
-        printContentsOfJobStore(job_store=jobStore)
-
     # TODO: We can't actually do *anything* for non-file job stores.
 
 
diff --git a/src/toil/utils/toilDebugJob.py b/src/toil/utils/toilDebugJob.py
index 23dd3f1efe..960f6b4c99 100644
--- a/src/toil/utils/toilDebugJob.py
+++ b/src/toil/utils/toilDebugJob.py
@@ -15,6 +15,7 @@
 import logging
 
 import pprint
+import sys
 
 from toil.common import Config, Toil, parser_with_common_options
 from toil.jobStores.fileJobStore import FileJobStore
diff --git a/src/toil/utils/toilDestroyCluster.py b/src/toil/utils/toilDestroyCluster.py
index 4095e21cbf..7239084842 100644
--- a/src/toil/utils/toilDestroyCluster.py
+++ b/src/toil/utils/toilDestroyCluster.py
@@ -21,8 +21,8 @@
 logger = logging.getLogger(__name__)
 
 def main() -> None:
-    parser = parser_with_common_options(provisioner_options=True, jobstore_option=False)
-    options = parser.parse_args(prog="toil destroy-cluster")
+    parser = parser_with_common_options(provisioner_options=True, jobstore_option=False, prog="toil destroy-cluster")
+    options = parser.parse_args()
     set_logging_from_options(options)
 
     logger.info('Destroying cluster %s', options.clusterName)