Ib_logfiles are not copied on restore

Error 13 means permission problems, check that the files are owned by mysql:mysql. mysqld usually runs with “mysql” user, but in your case it can’t open ibdata1 or frm files.

About the ib_logfiles they are not needed when restoring the backup. Anyway, those two files should be created by the --apply-log parameter. Can you attach the full --apply-log output?