Shards not allocating after rolling upgrade

I have a 2 node cluster on Elasticsearch 5.6.12

I followed this upgrade guide: https://www.elastic.co/guide/en/elasticsearch/reference/5.6/rolling-upgrades.html

After running:

PUT _cluster/settings
{
  "transient": {
    "cluster.routing.allocation.enable": "all"
  }
}

GET _cat/health is still returning yellow cluster status and shards remain unallocated?

Never mind - it was a high disk watermark [90%] exceeded warning

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