Sometimes this issue occurs when restarting Nexus [my version is 2.0.5].
The following steps to clean Nexus mostly help to get it up and running again
# Clear archetype-metadata.xml
– Goto
– perform the following command “rm **/*/archetype-metadata.xml
# Clear repository-metadata.xml
– Goto
– perform the following command “rm **/*/repository-metadata.xml
# Clean .nexus/attributes directories with size 0
– Goto
– perform the following command “find . -type f -size 0 |xargs rm”
After this, restart the service via ” sudo service nexus restart”