Upgrading from 5.6 to 6.x

when im trying to upgrade from 5.6 to 6.x im getting some errors im trying to do a rolling upgrade
below i have given the error which im getting even though i havent installed any plugins

[2018-06-27T05:48:38,655][INFO ][o.e.p.PluginsService ] [es01_node] loaded module [transport-netty4]
[2018-06-27T05:48:38,655][INFO ][o.e.p.PluginsService ] [es01_node] loaded module [tribe]
[2018-06-27T05:48:38,656][INFO ][o.e.p.PluginsService ] [es01_node] loaded module [x-pack-core]
[2018-06-27T05:48:38,656][INFO ][o.e.p.PluginsService ] [es01_node] loaded module [x-pack-deprecation]
[2018-06-27T05:48:38,656][INFO ][o.e.p.PluginsService ] [es01_node] loaded module [x-pack-graph]
[2018-06-27T05:48:38,656][INFO ][o.e.p.PluginsService ] [es01_node] loaded module [x-pack-logstash]
[2018-06-27T05:48:38,656][INFO ][o.e.p.PluginsService ] [es01_node] loaded module [x-pack-ml]
[2018-06-27T05:48:38,656][INFO ][o.e.p.PluginsService ] [es01_node] loaded module [x-pack-monitoring]
[2018-06-27T05:48:38,656][INFO ][o.e.p.PluginsService ] [es01_node] loaded module [x-pack-rollup]
[2018-06-27T05:48:38,656][INFO ][o.e.p.PluginsService ] [es01_node] loaded module [x-pack-security]
[2018-06-27T05:48:38,656][INFO ][o.e.p.PluginsService ] [es01_node] loaded module [x-pack-sql]
[2018-06-27T05:48:38,656][INFO ][o.e.p.PluginsService ] [es01_node] loaded module [x-pack-upgrade]
[2018-06-27T05:48:38,656][INFO ][o.e.p.PluginsService ] [es01_node] loaded module [x-pack-watcher]
[2018-06-27T05:48:38,657][INFO ][o.e.p.PluginsService ] [es01_node] no plugins loaded
[2018-06-27T05:48:42,118][ERROR][o.e.b.Bootstrap ] Exception
java.lang.IllegalArgumentException: unknown setting [path.conf] please check that any required plugins are installed, or check the breaking changes documentation for removed settings
at org.elasticsearch.common.settings.AbstractScopedSettings.validate(AbstractScopedSettings.java:344) ~[elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.common.settings.AbstractScopedSettings.validate(AbstractScopedSettings.java:308) ~[elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.common.settings.AbstractScopedSettings.validate(AbstractScopedSettings.java:282) ~[elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.common.settings.SettingsModule.(SettingsModule.java:135) ~[elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.node.Node.(Node.java:339) ~[elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.node.Node.(Node.java:252) ~[elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.bootstrap.Bootstrap$5.(Bootstrap.java:213) ~[elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.bootstrap.Bootstrap.setup(Bootstrap.java:213) ~[elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.bootstrap.Bootstrap.init(Bootstrap.java:326) [elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.bootstrap.Elasticsearch.init(Elasticsearch.java:136) [elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.bootstrap.Elasticsearch.execute(Elasticsearch.java:127) [elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.cli.EnvironmentAwareCommand.execute(EnvironmentAwareCommand.java:86) [elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.cli.Command.mainWithoutErrorHandling(Command.java:124) [elasticsearch-cli-6.3.0.jar:6.3.0]
at org.elasticsearch.cli.Command.main(Command.java:90) [elasticsearch-cli-6.3.0.jar:6.3.0]
at org.elasticsearch.bootstrap.Elasticsearch.main(Elasticsearch.java:93) [elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.bootstrap.Elasticsearch.main(Elasticsearch.java:86) [elasticsearch-6.3.0.jar:6.3.0]
[2018-06-27T05:48:42,125][WARN ][o.e.b.ElasticsearchUncaughtExceptionHandler] [es01_node] uncaught exception in thread [main]
org.elasticsearch.bootstrap.StartupException: java.lang.IllegalArgumentException: unknown setting [path.conf] please check that any required plugins are installed, or check the breaking changes documentation for removed settings
at org.elasticsearch.bootstrap.Elasticsearch.init(Elasticsearch.java:140) ~[elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.bootstrap.Elasticsearch.execute(Elasticsearch.java:127) ~[elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.cli.EnvironmentAwareCommand.execute(EnvironmentAwareCommand.java:86) ~[elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.cli.Command.mainWithoutErrorHandling(Command.java:124) ~[elasticsearch-cli-6.3.0.jar:6.3.0]
at org.elasticsearch.cli.Command.main(Command.java:90) ~[elasticsearch-cli-6.3.0.jar:6.3.0]
at org.elasticsearch.bootstrap.Elasticsearch.main(Elasticsearch.java:93) ~[elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.bootstrap.Elasticsearch.main(Elasticsearch.java:86) ~[elasticsearch-6.3.0.jar:6.3.0]
Caused by: java.lang.IllegalArgumentException: unknown setting [path.conf] please check that any required plugins are installed, or check the breaking changes documentation for removed settings
at org.elasticsearch.common.settings.AbstractScopedSettings.validate(AbstractScopedSettings.java:344) ~[elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.common.settings.AbstractScopedSettings.validate(AbstractScopedSettings.java:308) ~[elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.common.settings.AbstractScopedSettings.validate(AbstractScopedSettings.java:282) ~[elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.common.settings.SettingsModule.(SettingsModule.java:135) ~[elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.node.Node.(Node.java:339) ~[elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.node.Node.(Node.java:252) ~[elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.bootstrap.Bootstrap$5.(Bootstrap.java:213) ~[elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.bootstrap.Bootstrap.setup(Bootstrap.java:213) ~[elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.bootstrap.Bootstrap.init(Bootstrap.java:326) ~[elasticsearch-6.3.0.jar:6.3.0]
at org.elasticsearch.bootstrap.Elasticsearch.init(Elasticsearch.java:136) ~[elasticsearch-6.3.0.jar:6.3.0]

Please see https://www.elastic.co/guide/en/elasticsearch/reference/6.3/breaking_60_packaging_changes.html#_literal_path_conf_literal_is_no_longer_a_configurable_setting

ailed_allocation_attempts" : 5,
"details" : "failed recovery, failure RecoveryFailedException[[prirequestlog-2018.05.22][1]: Recovery failed from {es01_node}{rq7WtIWjRBGSaYPjz54t5A}{mXEEmLcSQYupBlkCr_ou3w}{xx.xx.xx.xxx}{xx.xx.xx.xx:9300}{ml.machine_memory=4145360896, ml.max_open_jobs=20, xpack.installed=true, ml.enabled=true} into {es02_node}{Pt3tgCviQke3HLksk-xY0w}{lSLI_axFRXC7NF6SO6lt6w}{xxx.xxx.xx.xxx}{xx.xxx.xx.xx:9300}{ml.machine_memory=4145360896, xpack.installed=true, ml.max_open_jobs=20, ml.enabled=true}]; nested: RemoteTransportException[[es01_node][xx.xxxx.xx.xx:9300][internal:index/shard/recovery/start_recovery]]; nested: RecoveryEngineException[Phase[1] prepare target for translog failed]; nested: RemoteTransportException[[es02_node][xx.xx.xx.xx:9300][internal:index/shard/recovery/prepare_translog]]; nested: IllegalStateException[commit doesn't contain history uuid]; ",

"decision" : "NO",
"explanation" : "shard has exceeded the maximum number of retries [5] on failed allocation attempts - manually call [/_cluster/reroute?retry_failed=true] to retry, [unassigned_info[[reason=ALLOCATION_FAILED], at[2018-06-28T08:07:34.551Z], failed_attempts[5], delayed=false, details[failed recovery, failure RecoveryFailedException[[prirequestlog-2018.05.22][1]: Recovery failed from {es01_node}{rq7WtIWjRBGSaYPjz54t5A}{mXEEmLcSQYupBlkCr_ou3w}{xx.xx.xx.xx}{xx.xx.xx.xx:9300}{ml.machine_memory=4145360896, ml.max_open_jobs=20, xpack.installed=true, ml.enabled=true} into {es02_node}{Pt3tgCviQke3HLksk-xY0w}{lSLI_axFRXC7NF6SO6lt6w}{xx.xx.xx.xx}{xx.xx.xx.xx:9300}{ml.machine_memory=4145360896, xpack.installed=true, ml.max_open_jobs=20, ml.enabled=true}]; nested: RemoteTransportException[[es01_node][xx.xx.xx.xx:9300][internal:index/shard/recovery/start_recovery]]; nested: RecoveryEngineException[Phase[1] prepare target for translog failed]; nested: RemoteTransportException[[es02_node][xx.xx.xx.xx:9300][internal:index/shard/recovery/prepare_translog]]; nested: IllegalStateException[commit doesn't contain history uuid]; ], allocation_status[no_attempt]]

im getting this error when i run this curl -XGET localhost:9200/_cluster/allocation/explain?pretty

This is a known issue https://github.com/elastic/elasticsearch/issues/31482. It was fixed and released in v6.3.1. Can you please upgrade to the latest version, then issue POST /_cluster/reroute?retry_failed=true?

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