Neo4j WARNING: Max 1024 open files allowed, minimum of 40 000 recommended. See the Neo4j manual

As mentioned in this issue comment and fixed by this commit, since Neo4J 3.1,

you can add a line in /etc/default/neo4j:

NEO4J_ULIMIT_NOFILE=60000

to set the ulimit setting (60000 open files) for the service.

There is no need anymore to use /etc/security/limits.conf on debian to set the number of open files.