Why all the Indices not upgraded in ES 6.1.1 after upgradation from 5.4.1?

Elastic Stack Elasticsearch
1

I have upgraded data from 5.4.1 to 6.1.1 using Full Cluster Restart
But all the indices not coming in ES 6.1.1

These are the steps that I followed:

1. Start ES 5.4.1 and Kibana 5.4.1 
2. Go to DevTools
3. Run 
PUT _cluster/settings
{
  "persistent": {
    "cluster.routing.allocation.enable": "none"
  }
}

4. Stop indexing and perform a synced flush.
Performing a synced-flush speeds up shard recovery.
POST _flush/synced

5. Shutdown ES and Kibana (5.4.1)
6. Download and unzip ES and Kibana 6.1.1.
7. Put configuration similar configurations of config/elasticsearch.yml and config/kibana.yml of 5.4.1 to 6.1.1
8. Upgrade any plugins: 
Use the elasticsearch-plugin script to install the upgraded version of each installed Elasticsearch plugin. All plugins must be upgraded when you upgrade a node.
9. Start ES 6.1.1 and Kibana 6.1.1 nodes
10. Copy elasticsearch-5.4.1\elasticsearch-5.4.1\data to elasticsearch-6.1.1\elasticsearch-6.1.1\data
11. Start each upgraded node.

If you have dedicated master nodes, start them first and wait for them to form a cluster and elect a master before proceeding with your data nodes. You can check progress by looking at the logs.
As soon as the minimum number of master-eligible nodes have discovered each other, they form a cluster and elect a master. At that point, you can use _cat/health and _cat/nodes to monitor nodes joining the cluster:
GET _cat/health
GET _cat/nodes
12. Reenable allocation
When all nodes have joined the cluster and recovered their primary shards, reenable allocation.
PUT _cluster/settings
{
  "persistent": {
    "cluster.routing.allocation.enable": "all"
  }
}
13. You can monitor progress with the _cat/health and _cat/recovery APIs:
GET _cat/health
GET _cat/recovery
14. Run curl command in cmd 
curl -XDELETE  http://10.1.54.108:9400/.kibana
15. Restart kibana 6.1.1 server
2

Can you explain what you mean by this please?

3

I have approx 30 - 40 indices in ES version 5.4.1 but after upgrading it to ES version 6.1.1 Its showing me less number of Index

4

What do the logs show?

5

[2018-01-15T13:22:18,007][WARN ][o.e.d.c.ParseField ] Deprecated field [all_fields] used, replaced by [Set [fields] to * instead]
[2018-01-15T13:22:18,048][WARN ][o.e.d.c.ParseField ] Deprecated field [all_fields] used, replaced by [Set [fields] to * instead]
[2018-01-15T13:22:18,084][WARN ][o.e.d.c.ParseField ] Deprecated field [inline] used, expected [source] instead
[2018-01-15T13:22:18,086][WARN ][o.e.d.c.ParseField ] Deprecated field [inline] used, expected [source] instead
[2018-01-15T13:34:26,840][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T13:34:27,712][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T13:34:27,720][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T13:34:27,966][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T13:34:28,632][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T13:35:26,427][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T13:35:27,167][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T13:35:27,192][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T13:35:31,101][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T13:35:39,863][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T13:36:23,067][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T13:36:24,012][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T13:36:24,085][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T14:38:45,373][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T14:38:46,798][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T14:38:46,839][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T14:38:46,909][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T14:38:47,632][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T14:42:44,186][WARN ][o.e.d.c.ParseField ] Deprecated field [all_fields] used, replaced by [Set [fields] to * instead]
[2018-01-15T14:42:44,212][WARN ][o.e.d.c.ParseField ] Deprecated field [all_fields] used, replaced by [Set [fields] to * instead]
[2018-01-15T14:42:44,220][WARN ][o.e.d.c.ParseField ] Deprecated field [inline] used, expected [source] instead
[2018-01-15T14:42:44,313][WARN ][o.e.d.c.ParseField ] Deprecated field [inline] used, expected [source] instead
[2018-01-15T15:20:07,047][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T15:20:07,930][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T15:23:52,872][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T15:23:53,502][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T15:25:17,413][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T15:25:17,911][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T15:27:07,943][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T15:27:09,113][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T15:33:33,938][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T15:36:59,504][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T15:51:22,941][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T15:51:30,762][WARN ][o.e.d.c.ParseField ] Deprecated field [all_fields] used, replaced by [Set [fields] to * instead]
[2018-01-15T15:51:30,773][WARN ][o.e.d.c.ParseField ] Deprecated field [inline] used, expected [source] instead
[2018-01-15T15:51:30,810][WARN ][o.e.d.c.ParseField ] Deprecated field [all_fields] used, replaced by [Set [fields] to * instead]
[2018-01-15T15:51:30,863][WARN ][o.e.d.c.ParseField ] Deprecated field [inline] used, expected [source] instead
[2018-01-15T15:54:36,018][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T15:55:54,101][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T17:54:40,992][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T17:54:42,303][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T17:55:07,597][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T17:55:08,482][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T17:55:45,124][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T17:55:45,771][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
[2018-01-15T17:56:09,392][WARN ][o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]

6

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