Based on my research the errors in logs seem to be a known issue with embedded mode. Please take a look at this.
As resolution, i would suggest following options:
Using external HBase and Solr5.
If you are looking to use Atlas for experimentation, try using BerkeleyDB and Elastic search combination. Use the attached properties file (rename it to atlas-application.properties and drop it in the conf directory).
Also try downloading HDP sandbox if you wish to investigate features of Atlas and test out the integrations with Ranger and Hive