{"action":"created","issue":{"url":"https://api.github.com/repos/BD2KGenomics/protect/issues/62","repository_url":"https://api.github.com/repos/BD2KGenomics/protect","labels_url":"https://api.github.com/repos/BD2KGenomics/protect/issues/62/labels{/name}","comments_url":"https://api.github.com/repos/BD2KGenomics/protect/issues/62/comments","events_url":"https://api.github.com/repos/BD2KGenomics/protect/issues/62/events","html_url":"https://github.com/BD2KGenomics/protect/issues/62","id":162200426,"number":62,"title":"No space left on device","user":{"login":"Jeltje","id":5482232,"avatar_url":"https://avatars.githubusercontent.com/u/5482232?v=3","gravatar_id":"","url":"https://api.github.com/users/Jeltje","html_url":"https://github.com/Jeltje","followers_url":"https://api.github.com/users/Jeltje/followers","following_url":"https://api.github.com/users/Jeltje/following{/other_user}","gists_url":"https://api.github.com/users/Jeltje/gists{/gist_id}","starred_url":"https://api.github.com/users/Jeltje/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Jeltje/subscriptions","organizations_url":"https://api.github.com/users/Jeltje/orgs","repos_url":"https://api.github.com/users/Jeltje/repos","events_url":"https://api.github.com/users/Jeltje/events{/privacy}","received_events_url":"https://api.github.com/users/Jeltje/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-06-24T18:07:05Z","updated_at":"2016-06-24T18:10:43Z","closed_at":null,"body":"ProTECT exits with \r\n```\r\nIOError: [Errno 28] No space left on device\r\nERROR:toil.worker:Exiting the worker because of a failed jobWrapper on host jeltje-tb\r\n```\r\nHowever, my filesystem is fine (jobstore and output are supposed to go to /mnt/data):\r\n```\r\nFilesystem      Size  Used Avail Use% Mounted on\r\nudev             24G     0   24G   0% /dev\r\ntmpfs           4.8G  247M  4.6G   6% /run\r\n/dev/vda1        49G   19G   31G  38% /\r\ntmpfs            24G     0   24G   0% /dev/shm\r\ntmpfs           5.0M     0  5.0M   0% /run/lock\r\ntmpfs            24G     0   24G   0% /sys/fs/cgroup\r\n/dev/vdb1       2.0T  1.3T  554G  71% /mnt\r\ntmpfs           4.8G     0  4.8G   0% /run/user/1000\r\n```\r\nThere is a suspicious `Unable to acquire lock on /tmp/toil-0fb5cb74-48c9-408d-b0e5-5c3cf37cce33/cache-0fb5cb74-48c9-408d-b0e5-5c3cf37cce33/.cacheLock` so I'm wondering if this is docker being greedy?\r\nFull log at http://hgwdev.cse.ucsc.edu/~jeltje/toil/protect.nospace\r\n"},"comment":{"url":"https://api.github.com/repos/BD2KGenomics/protect/issues/comments/228419057","html_url":"https://github.com/BD2KGenomics/protect/issues/62#issuecomment-228419057","issue_url":"https://api.github.com/repos/BD2KGenomics/protect/issues/62","id":228419057,"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":"2016-06-24T18:10:42Z","updated_at":"2016-06-24T18:10:42Z","body":"/tmp is on /dev/vda1 which only has 31GB free.\r\n Most of the aligners ask for 60GB each right now so you can't run.\r\nI'm working on #4 right now to make it a little better.\r\n\r\nFor now, you can do something similar to what is in jenkins.sh\r\n`mkdir -p /mnt/ephemeral/tmp && export TMPDIR=/mnt/ephemeral/tmp`"}}
{"actor":{"display_login":"arkal"}}