{"action":"created","issue":{"url":"https://api.github.com/repos/tseemann/shovill/issues/80","repository_url":"https://api.github.com/repos/tseemann/shovill","labels_url":"https://api.github.com/repos/tseemann/shovill/issues/80/labels{/name}","comments_url":"https://api.github.com/repos/tseemann/shovill/issues/80/comments","events_url":"https://api.github.com/repos/tseemann/shovill/issues/80/events","html_url":"https://github.com/tseemann/shovill/issues/80","id":329304835,"node_id":"MDU6SXNzdWUzMjkzMDQ4MzU=","number":80,"title":"stalled running kmc in for loop in shell ","user":{"login":"indexofire","id":169425,"node_id":"MDQ6VXNlcjE2OTQyNQ==","avatar_url":"https://avatars0.githubusercontent.com/u/169425?v=4","gravatar_id":"","url":"https://api.github.com/users/indexofire","html_url":"https://github.com/indexofire","followers_url":"https://api.github.com/users/indexofire/followers","following_url":"https://api.github.com/users/indexofire/following{/other_user}","gists_url":"https://api.github.com/users/indexofire/gists{/gist_id}","starred_url":"https://api.github.com/users/indexofire/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/indexofire/subscriptions","organizations_url":"https://api.github.com/users/indexofire/orgs","repos_url":"https://api.github.com/users/indexofire/repos","events_url":"https://api.github.com/users/indexofire/events{/privacy}","received_events_url":"https://api.github.com/users/indexofire/received_events","type":"User","site_admin":false},"labels":[{"id":437223455,"node_id":"MDU6TGFiZWw0MzcyMjM0NTU=","url":"https://api.github.com/repos/tseemann/shovill/labels/question","name":"question","color":"cc317c","default":true}],"state":"closed","locked":false,"assignee":{"login":"tseemann","id":453972,"node_id":"MDQ6VXNlcjQ1Mzk3Mg==","avatar_url":"https://avatars2.githubusercontent.com/u/453972?v=4","gravatar_id":"","url":"https://api.github.com/users/tseemann","html_url":"https://github.com/tseemann","followers_url":"https://api.github.com/users/tseemann/followers","following_url":"https://api.github.com/users/tseemann/following{/other_user}","gists_url":"https://api.github.com/users/tseemann/gists{/gist_id}","starred_url":"https://api.github.com/users/tseemann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tseemann/subscriptions","organizations_url":"https://api.github.com/users/tseemann/orgs","repos_url":"https://api.github.com/users/tseemann/repos","events_url":"https://api.github.com/users/tseemann/events{/privacy}","received_events_url":"https://api.github.com/users/tseemann/received_events","type":"User","site_admin":false},"assignees":[{"login":"tseemann","id":453972,"node_id":"MDQ6VXNlcjQ1Mzk3Mg==","avatar_url":"https://avatars2.githubusercontent.com/u/453972?v=4","gravatar_id":"","url":"https://api.github.com/users/tseemann","html_url":"https://github.com/tseemann","followers_url":"https://api.github.com/users/tseemann/followers","following_url":"https://api.github.com/users/tseemann/following{/other_user}","gists_url":"https://api.github.com/users/tseemann/gists{/gist_id}","starred_url":"https://api.github.com/users/tseemann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tseemann/subscriptions","organizations_url":"https://api.github.com/users/tseemann/orgs","repos_url":"https://api.github.com/users/tseemann/repos","events_url":"https://api.github.com/users/tseemann/events{/privacy}","received_events_url":"https://api.github.com/users/tseemann/received_events","type":"User","site_admin":false}],"milestone":null,"comments":1,"created_at":"2018-06-05T05:16:10Z","updated_at":"2018-06-06T00:18:34Z","closed_at":"2018-06-05T09:17:25Z","author_association":"NONE","body":"when assembling multiple bacteria genomes,  I used to use for loop in terminal like this in server:\r\n\r\n```bash\r\n$ nohup sh -c 'for i in ...; do shovill --R1 ... --R2 ... ; done' &\r\n```\r\n\r\nHowever, the pipeline would stalled sometimes when running kmc. If I just run shovill to assemble the stalled genome, it passed kmc check, and everything is ok. My server has 128g ram and no seperated /tmp partition ( /tmp is in the / filesystem, so I think the disk space is enough). Any suggestion? Thanks"},"comment":{"url":"https://api.github.com/repos/tseemann/shovill/issues/comments/394900625","html_url":"https://github.com/tseemann/shovill/issues/80#issuecomment-394900625","issue_url":"https://api.github.com/repos/tseemann/shovill/issues/80","id":394900625,"node_id":"MDEyOklzc3VlQ29tbWVudDM5NDkwMDYyNQ==","user":{"login":"indexofire","id":169425,"node_id":"MDQ6VXNlcjE2OTQyNQ==","avatar_url":"https://avatars0.githubusercontent.com/u/169425?v=4","gravatar_id":"","url":"https://api.github.com/users/indexofire","html_url":"https://github.com/indexofire","followers_url":"https://api.github.com/users/indexofire/followers","following_url":"https://api.github.com/users/indexofire/following{/other_user}","gists_url":"https://api.github.com/users/indexofire/gists{/gist_id}","starred_url":"https://api.github.com/users/indexofire/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/indexofire/subscriptions","organizations_url":"https://api.github.com/users/indexofire/orgs","repos_url":"https://api.github.com/users/indexofire/repos","events_url":"https://api.github.com/users/indexofire/events{/privacy}","received_events_url":"https://api.github.com/users/indexofire/received_events","type":"User","site_admin":false},"created_at":"2018-06-06T00:18:34Z","updated_at":"2018-06-06T00:18:34Z","author_association":"NONE","body":"got that, it had been updated in the master branch. thanks anyway, Hope 1.0 comes out soon."}}
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