What steps will reproduce the problem? 1. cd to an already existing git repository that uses Github as a remote, with the remote format similar to git@github.com:user/repo.git 2. git annex init 3. git annex status What is the expected output? What do you see instead? $ git annex status supported backends: SHA256 SHA1 SHA512 SHA224 SHA384 SHA256E SHA1E SHA512E SHA224E SHA384E WORM URL supported remote types: git S3 bup directory rsync web hook trusted repositories: Invalid command: 'git-annex-shell 'configlist' '/~/dlo/objectifier.git'' You appear to be using ssh to clone a git:// URL. Make sure your core.gitProxy config option and the GIT_PROXY_COMMAND environment variable are NOT set. Command ssh ["-S","/Users/dan/Documents/Web/objectifier/.git/annex/ssh/git@github.com","-o","ControlMaster=auto","-o","ControlPersist=yes","git@github.com","git-annex-shell 'configlist' '/~/dlo/objectifier.git'"] failed; exit code 1 0 # ... other stuff that isn't relevant What version of git-annex are you using? On what operating system? git-annex-3.20120825 Max OS X 10.8.1 > [[done]]; see comments --[[Joey]]