I'm facing the following issue while upgrading pgsql 9.6 to pgsql 13.
It's saying database "template0" "template1" does not exist on source 9.6, please advise.
You might want to just forget doing a pg_upgrade migration and do a pg_dumpall one instead. The missing template databases on the existing cluster shouldn't be noticed.
You can decide how important missing the directories are to you, since that shouldn't happen outside someone going in and "rm'ing" them.