ElasticSearch 2.4.1 to 5.0.2 upgrade fails

Hello all
I am trying to upgrade my ES install.
I stopped all the nodes in the cluster, upgraded one and tries to start it.
However, it fails with a lot of those errors :

[2016-11-30T15:28:36,932][INFO ][o.e.n.Node ] [es-node-iam-rec-002-1] initializing ...
[2016-11-30T15:28:37,024][INFO ][o.e.e.NodeEnvironment ] [es-node-iam-rec-002-1] using [1] data paths, mounts [[/var/opt/novell (/dev/sdc1)]], net usable_space [6.4gb], net total_space [9.8gb], spins? [possibly], types [ext3]
[2016-11-30T15:28:37,024][INFO ][o.e.e.NodeEnvironment ] [es-node-iam-rec-002-1] heap size [123.7mb], compressed ordinary object pointers [true]
[2016-11-30T15:28:37,109][INFO ][o.e.n.Node ] [es-node-iam-rec-002-1] version[5.0.2], pid[3025], build[f6b4951/2016-11-24T10:07:18.101Z], OS[Linux/3.0.101-65-default/amd64], JVM[Oracle Corporation/Java HotSpot(TM) 64-Bit Server VM/1.8.0_66/25.66-b17]
[2016-11-30T15:28:38,182][INFO ][o.e.p.PluginsService ] [es-node-iam-rec-002-1] loaded module [aggs-matrix-stats]
[2016-11-30T15:28:38,182][INFO ][o.e.p.PluginsService ] [es-node-iam-rec-002-1] loaded module [ingest-common]
[2016-11-30T15:28:38,182][INFO ][o.e.p.PluginsService ] [es-node-iam-rec-002-1] loaded module [lang-expression]
[2016-11-30T15:28:38,183][INFO ][o.e.p.PluginsService ] [es-node-iam-rec-002-1] loaded module [lang-groovy]
[2016-11-30T15:28:38,183][INFO ][o.e.p.PluginsService ] [es-node-iam-rec-002-1] loaded module [lang-mustache]
[2016-11-30T15:28:38,183][INFO ][o.e.p.PluginsService ] [es-node-iam-rec-002-1] loaded module [lang-painless]
[2016-11-30T15:28:38,183][INFO ][o.e.p.PluginsService ] [es-node-iam-rec-002-1] loaded module [percolator]
[2016-11-30T15:28:38,183][INFO ][o.e.p.PluginsService ] [es-node-iam-rec-002-1] loaded module [reindex]
[2016-11-30T15:28:38,183][INFO ][o.e.p.PluginsService ] [es-node-iam-rec-002-1] loaded module [transport-netty3]
[2016-11-30T15:28:38,183][INFO ][o.e.p.PluginsService ] [es-node-iam-rec-002-1] loaded module [transport-netty4]
[2016-11-30T15:28:38,183][INFO ][o.e.p.PluginsService ] [es-node-iam-rec-002-1] no plugins loaded
[2016-11-30T15:28:40,563][INFO ][o.e.c.u.IndexFolderUpgrader] [clara_users/KZs9OJNLTlySLaBjq0JFYg] upgrading [/var/opt/novell/idm/rbpm/vinci_elasticsearch_data/es-cluster-iam-rec/nodes/0/indices/clara_users] to new naming convention
[2016-11-30T15:28:40,565][ERROR][o.e.g.GatewayMetaState ] [es-node-iam-rec-002-1] failed to read local state, exiting...
java.nio.file.FileSystemException: /var/opt/novell/idm/rbpm/vinci_elasticsearch_data/es-cluster-iam-rec/nodes/0/indices/clara_users -> /var/opt/novell/idm/rbpm/vinci_elasticsearch_data/es-cluster-iam-rec/nodes/0/indices/KZs9OJNLTlySLaBjq0JFYg: Directory not empty
at sun.nio.fs.UnixException.translateToIOException(UnixException.java:91) ~[?:?]
at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102) ~[?:?]
at sun.nio.fs.UnixCopyFile.move(UnixCopyFile.java:396) ~[?:?]
at sun.nio.fs.UnixFileSystemProvider.move(UnixFileSystemProvider.java:262) ~[?:?]
at java.nio.file.Files.move(Files.java:1395) ~[?:1.8.0_66]

I have 4 nodes in my cluster and 6 index for a total of only 4 Go of data.
I read and followed the documentation and can't find what i did wrong...
Thanks

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