Bench --site migrate failed due to "Unknown column 'apply_user_permissions' in 'field list'"

bench migrate command exited with the following error, is there anything I can do to solve?

$ bench --site site1.local migrate
Migrating site1.local
Executing execute:frappe.reload_doc('core', 'doctype', 'docfield', force=True) #2018-02-20 in site1.local (1bd3e0294da19198)
Success
Executing frappe.patches.v10_0.refactor_social_login_keys in site1.local (1bd3e0294da19198)
Success
Executing frappe.patches.v10_0.enable_chat_by_default_within_system_settings in site1.local (1bd3e0294da19198)
Success
Executing frappe.patches.v10_0.remove_custom_field_for_disabled_domain in site1.local (1bd3e0294da19198)
Success
Executing execute:frappe.delete_doc("Page", "chat") in site1.local (1bd3e0294da19198)
Success
Executing frappe.patches.v11_0.drop_column_apply_user_permissions in site1.local (1bd3e0294da19198)
Success
Executing erpnext.patches.v11_0.rename_production_order_to_work_order in site1.local (1bd3e0294da19198)
Traceback (most recent call last):
  File "/usr/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/usr/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/home/frappe/frappe-bench/apps/frappe/frappe/utils/bench_helper.py", line 97, in <module>
    main()
  File "/home/frappe/frappe-bench/apps/frappe/frappe/utils/bench_helper.py", line 18, in main
    click.Group(commands=commands)(prog_name='bench')
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/click/decorators.py", line 17, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/commands/__init__.py", line 25, in _func
    ret = f(frappe._dict(ctx.obj), *args, **kwargs)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/commands/site.py", line 222, in migrate
    migrate(context.verbose, rebuild_website=rebuild_website)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/migrate.py", line 39, in migrate
    frappe.modules.patch_handler.run_all()
  File "/home/frappe/frappe-bench/apps/frappe/frappe/modules/patch_handler.py", line 29, in run_all
    if not run_single(patchmodule = patch):
  File "/home/frappe/frappe-bench/apps/frappe/frappe/modules/patch_handler.py", line 63, in run_single
    return execute_patch(patchmodule, method, methodargs)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/modules/patch_handler.py", line 83, in execute_patch
    frappe.get_attr(patchmodule.split()[0] + ".execute")()
  File "/home/frappe/frappe-bench/apps/erpnext/erpnext/patches/v11_0/rename_production_order_to_work_order.py", line 11, in execute
    frappe.reload_doc('manufacturing', 'doctype', 'work_order')
  File "/home/frappe/frappe-bench/apps/frappe/frappe/__init__.py", line 699, in reload_doc
    return frappe.modules.reload_doc(module, dt, dn, force=force, reset_permissions=reset_permissions)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/modules/utils.py", line 155, in reload_doc
    return import_files(module, dt, dn, force=force, reset_permissions=reset_permissions)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/modules/import_file.py", line 19, in import_files
    reset_permissions=reset_permissions)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/modules/import_file.py", line 24, in import_file
    ret = import_file_by_path(path, force, pre_process=pre_process, reset_permissions=reset_permissions)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/modules/import_file.py", line 58, in import_file_by_path
    ignore_version=ignore_version, reset_permissions=reset_permissions)
  File "/home/frappe/frappe-bench/apps/frappe/frappe/modules/import_file.py", line 132, in import_doc
    doc.insert()
  File "/home/frappe/frappe-bench/apps/frappe/frappe/model/document.py", line 237, in insert
    d.db_insert()
  File "/home/frappe/frappe-bench/apps/frappe/frappe/model/base_document.py", line 303, in db_insert
    ), list(d.values()))
  File "/home/frappe/frappe-bench/apps/frappe/frappe/database.py", line 195, in sql
    self._cursor.execute(query, values)
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/pymysql/cursors.py", line 165, in execute
    result = self._query(query)
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/pymysql/cursors.py", line 321, in _query
    conn.query(q)
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/pymysql/connections.py", line 860, in query
    self._affected_rows = self._read_query_result(unbuffered=unbuffered)
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/pymysql/connections.py", line 1061, in _read_query_result
    result.read()
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/pymysql/connections.py", line 1349, in read
    first_packet = self.connection._read_packet()
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/pymysql/connections.py", line 1018, in _read_packet
    packet.check_error()
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/pymysql/connections.py", line 384, in check_error
    err.raise_mysql_exception(self._data)
  File "/home/frappe/frappe-bench/env/local/lib/python2.7/site-packages/pymysql/err.py", line 107, in raise_mysql_exception
    raise errorclass(errno, errval)
pymysql.err.InternalError: (1054, u"Unknown column 'apply_user_permissions' in 'field list'")

Welcome to ERPNext oxwivi

Search on ‘pymysql.err.InternalError: (1054, u"Unknown column’ for clues what to try?

edit: For eg Bench update mysql InternalError : Unknown column reserve_warehouse in field list

@oxwivi When I had same issue I commented out that Particular Patch and ran update after all the patch ran I removed comment ran once again it worked for me

I was migrating from ERPNext.com instance, it literally only had the first time setup done with zero data. Switching to develop branch made the problem go away.