try this :
1) create your subquery
$subquery = $this->_em->createQueryBuilder()
->select('t.id')
->from('yourBundle:Task', 't')
->innerjoin('t.user','u')
->where('u.id = 1')
->getDQL();
2) after create your query
$query = $this->_em->createQueryBuilder();
$query->select('l')
->from('yourBundle:Layer', 'l')
->where($query->expr()->notIn('l.id', $subquery))
....;
I tested it and it works :)
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