diff --git a/snakemake/scheduler.py b/snakemake/scheduler.py
index c26f39e9a..1b3ac8669 100644
--- a/snakemake/scheduler.py
+++ b/snakemake/scheduler.py
@@ -43,6 +43,11 @@ def cumsum(iterable, zero=[0]):
     "Exiting because a job execution failed. " "Look above for error message"
 )
 
+_ERROR_MSG_ISSUE_823 = (
+    "BUG: Out of jobs ready to be started, but not all files built yet."
+    " Please check https://github.com/snakemake/snakemake/issues/823 for more information."
+)
+
 
 class DummyRateLimiter(ContextDecorator):
     def __enter__(self):
@@ -470,11 +475,23 @@ def schedule(self):
                         return False
                     continue
 
-                # normal shutdown because all jobs have been finished
+                # all runnable jobs have finished, normal shutdown
                 if not needrun and (not running or self.workflow.immediate_submit):
                     self._executor.shutdown()
                     if errors:
                         logger.error(_ERROR_MSG_FINAL)
+                    # we still have unfinished jobs. this is not good. direct
+                    # user to github issue
+                    if self.remaining_jobs:
+                        logger.error(_ERROR_MSG_ISSUE_823)
+                        logger.error(
+                            "Remaining jobs:\n"
+                            + "\n".join(
+                                " - " + str(job) + ": " + ", ".join(job.output)
+                                for job in self.remaining_jobs
+                            )
+                        )
+                        return False
                     return not errors
 
                 # continue if no new job needs to be executed
diff --git a/tests/test_issue823_3/Snakefile b/tests/test_issue823_3/Snakefile
new file mode 100644
index 000000000..67f777b51
--- /dev/null
+++ b/tests/test_issue823_3/Snakefile
@@ -0,0 +1,9 @@
+rule all:
+    input:
+        "a.txt"
+
+checkpoint a:
+    output:
+        "a.txt"
+    shell:
+        "touch {output}"
diff --git a/tests/test_issue823_3/expected-results/a.txt b/tests/test_issue823_3/expected-results/a.txt
new file mode 100644
index 000000000..e69de29bb
diff --git a/tests/tests.py b/tests/tests.py
index bfa2503fa..547889599 100644
--- a/tests/tests.py
+++ b/tests/tests.py
@@ -887,6 +887,11 @@ def test_issue823_2():
     run(dpath("test_issue823_2"))
 
 
+@skip_on_windows
+def test_issue823_3():
+    run(dpath("test_issue823_3"))
+
+
 @skip_on_windows
 def test_pathlib():
     run(dpath("test_pathlib"))