diff --git a/cwltool/job.py b/cwltool/job.py
index e0368f194..fc69d17dd 100644
--- a/cwltool/job.py
+++ b/cwltool/job.py
@@ -100,7 +100,10 @@ def relink_initialworkdir(
                     pass
             elif os.path.isdir(host_outdir_tgt) and not vol.resolved.startswith("_:"):
                 ensure_writable(host_outdir_tgt, include_root=True)
-                shutil.rmtree(host_outdir_tgt)
+                try:
+                    shutil.rmtree(host_outdir_tgt)
+                except PermissionError:
+                    pass
             if not vol.resolved.startswith("_:"):
                 try:
                     os.symlink(vol.resolved, host_outdir_tgt)