The log is :

 Primary shard is not active or isn't assigned is a known node. Timeout: [1m]

you should look at that link:
http://www.elasticsearch.org/guide/en/elasticsearch/reference/current/index-modules-allocation.html
https://www.elastic.co/guide/en/elasticsearch/reference/5.x/disk-allocator.html
and that part in particular:

cluster.routing.allocation.disk.watermark.low controls the low watermark for disk usage. It defaults to 85%, meaning ES will not allocate new shards to nodes once they have more than 85% disk used. It can also be set to an absolute byte value (like 500mb) to prevent ES from allocating shards if less than the configured amount of space is available.
cluster.routing.allocation.disk.watermark.high controls the high watermark. It defaults to 90%, meaning ES will attempt to relocate shards to another node if the node disk usage rises above 90%. It can also be set to an absolute byte value (similar to the low watermark) to relocate shards once less than the configured amount of space is available on the node.