Annoyingly we need to check the permissions of the file before doing these opertations. Under some circumstances the index is rebuilt but the current user does not write the file (so it looks like the DB is doing it). So we only change the permissions of files we wrote which seems to solve the problem.
Annoyingly we need to check the permissions of the file before doing these opertations. Under some circumstances the index is rebuilt but the current user does not write the file (so it looks like the DB is doing it). So we only change the permissions of files we wrote which seems to solve the problem.

EnsemblGenomes/mysqlnaga