{"action":"created","issue":{"url":"https://api.github.com/repos/BD2KGenomics/toil/issues/1154","repository_url":"https://api.github.com/repos/BD2KGenomics/toil","labels_url":"https://api.github.com/repos/BD2KGenomics/toil/issues/1154/labels{/name}","comments_url":"https://api.github.com/repos/BD2KGenomics/toil/issues/1154/comments","events_url":"https://api.github.com/repos/BD2KGenomics/toil/issues/1154/events","html_url":"https://github.com/BD2KGenomics/toil/issues/1154","id":176792759,"number":1154,"title":"Workflow directories are not cleaned up","user":{"login":"hannes-ucsc","id":5143256,"avatar_url":"https://avatars.githubusercontent.com/u/5143256?v=3","gravatar_id":"","url":"https://api.github.com/users/hannes-ucsc","html_url":"https://github.com/hannes-ucsc","followers_url":"https://api.github.com/users/hannes-ucsc/followers","following_url":"https://api.github.com/users/hannes-ucsc/following{/other_user}","gists_url":"https://api.github.com/users/hannes-ucsc/gists{/gist_id}","starred_url":"https://api.github.com/users/hannes-ucsc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hannes-ucsc/subscriptions","organizations_url":"https://api.github.com/users/hannes-ucsc/orgs","repos_url":"https://api.github.com/users/hannes-ucsc/repos","events_url":"https://api.github.com/users/hannes-ucsc/events{/privacy}","received_events_url":"https://api.github.com/users/hannes-ucsc/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/BD2KGenomics/toil/labels/bug","name":"bug","color":"fc2929"},{"url":"https://api.github.com/repos/BD2KGenomics/toil/labels/caching","name":"caching","color":"bfe5bf"},{"url":"https://api.github.com/repos/BD2KGenomics/toil/labels/discuss","name":"discuss","color":"eb6420"},{"url":"https://api.github.com/repos/BD2KGenomics/toil/labels/mesos","name":"mesos","color":"d4c5f9"}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":23,"created_at":"2016-09-14T01:35:07Z","updated_at":"2016-10-01T11:14:37Z","closed_at":null,"body":"@Jeltje reports in https://github.com/BD2KGenomics/toil-scripts/issues/447 that the workflow directories are not being cleared up /var/lib/toil/toil-UUID. In a subsequent run, I've also seen on one of her workers that a previous workflow's directory was left on disk, a workflow that was terminated via Ctrl-C on the leader. It is possible the left overs from https://github.com/BD2KGenomics/toil-scripts/issues/447 were also caused by termination via Ctrl-C but that's not a reliable assumption.\n\nIt is also possible that the left-over workflow directories are breaking caching for subsequent workflows. @Jeltje and I saw the `assert cacheInfo.isBalanced` assert failing in a run where the leftovers were still present. An otherwise identical run on a clean cluster hasn't"},"comment":{"url":"https://api.github.com/repos/BD2KGenomics/toil/issues/comments/250906888","html_url":"https://github.com/BD2KGenomics/toil/issues/1154#issuecomment-250906888","issue_url":"https://api.github.com/repos/BD2KGenomics/toil/issues/1154","id":250906888,"user":{"login":"arkal","id":11653944,"avatar_url":"https://avatars.githubusercontent.com/u/11653944?v=3","gravatar_id":"","url":"https://api.github.com/users/arkal","html_url":"https://github.com/arkal","followers_url":"https://api.github.com/users/arkal/followers","following_url":"https://api.github.com/users/arkal/following{/other_user}","gists_url":"https://api.github.com/users/arkal/gists{/gist_id}","starred_url":"https://api.github.com/users/arkal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/arkal/subscriptions","organizations_url":"https://api.github.com/users/arkal/orgs","repos_url":"https://api.github.com/users/arkal/repos","events_url":"https://api.github.com/users/arkal/events{/privacy}","received_events_url":"https://api.github.com/users/arkal/received_events","type":"User","site_admin":false},"created_at":"2016-10-01T11:14:37Z","updated_at":"2016-10-01T11:14:37Z","body":"+∞ for all the time spent on this today.\r\n"}}
{"actor":{"display_login":"arkal"}}