Cluster state is yellow during restore process with ES 6

Elastic Stack Elasticsearch
1

I have recently migrated my elasticsearch to version 6 from version 2.4
After installing a new elasticsearch 6 cluster I am trying to restore data from a snapshot, but during the restore process the elasticsearch cluster status is yellow and not red. As per the docs it is supposed to be red when recovering primary shards.

Also the time to restore the snapshot has doubled after migration to ES6. With ES 2.4 it used to take approx 30 mins to restore and with ES 6 it now takes 67 mins approx. The size of the data, number of shards and settings are same, except that I have removed settings indices.recovery.concurrent_small_file_streams and indices.recovery.concurrent_file_streams as they have been removed.

Settings in elasticsearch.yml:

cloud.node.auto_attributes: true
cluster.name: elasticsearch
cluster.routing.allocation.awareness.attributes: aws_availability_zone
discovery.ec2.availability_zones: us-west-2a,us-west-2b,us-west-2c
discovery.ec2.endpoint: ec2.us-west-2.amazonaws.com
discovery.ec2.groups: data-index
discovery.ec2.host_type: private_ip
discovery.ec2.protocol: http
discovery.ec2.tag.Name: data-index
discovery.zen.hosts_provider: ec2
http.port: 9200
network.host: _ec2:privateIp_,_local_
node.name: ip-173-31-6-100
path.data: /data
path.logs: /var/log/elasticsearch
s3.client.default.endpoint: s3.us-west-2.amazonaws.com
s3.client.default.protocol: http
transport.tcp.port: 9300
xpack.ml.enabled: false
xpack.security.enabled: false

Settings used when creating repository:

{
  "type": "s3",
  "settings": {
    "bucket": "data-index-backup",
    "base_path": "data/es6test",
    "max_restore_bytes_per_sec": "0",
    "max_snapshot_bytes_per_sec": "0"
  }
}

Settings used with restore command:

{
  "include_global_state": false,
  "index_settings": {
	"index.number_of_replicas": "0",
	"index.refresh_interval": "-1"
  }
}

Cluster health output:

{
  "cluster_name": "elasticsearch",
  "status": "yellow",
  "timed_out": false,
  "number_of_nodes": 3,
  "number_of_data_nodes": 3,
  "active_primary_shards": 36,
  "active_shards": 42,
  "relocating_shards": 0,
  "initializing_shards": 45,
  "unassigned_shards": 33,
  "delayed_unassigned_shards": 0,
  "number_of_pending_tasks": 0,
  "number_of_in_flight_fetch": 0,
  "task_max_waiting_in_queue_millis": 0,
  "active_shards_percent_as_number": 35
}
2

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