{"action":"created","issue":{"url":"https://api.github.com/repos/marbl/canu/issues/114","repository_url":"https://api.github.com/repos/marbl/canu","labels_url":"https://api.github.com/repos/marbl/canu/issues/114/labels{/name}","comments_url":"https://api.github.com/repos/marbl/canu/issues/114/comments","events_url":"https://api.github.com/repos/marbl/canu/issues/114/events","html_url":"https://github.com/marbl/canu/issues/114","id":150627683,"number":114,"title":"Canu failed in SLRUM system when array ID is larger than 1000","user":{"login":"tangerzhang","id":6403754,"avatar_url":"https://avatars.githubusercontent.com/u/6403754?v=3","gravatar_id":"","url":"https://api.github.com/users/tangerzhang","html_url":"https://github.com/tangerzhang","followers_url":"https://api.github.com/users/tangerzhang/followers","following_url":"https://api.github.com/users/tangerzhang/following{/other_user}","gists_url":"https://api.github.com/users/tangerzhang/gists{/gist_id}","starred_url":"https://api.github.com/users/tangerzhang/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tangerzhang/subscriptions","organizations_url":"https://api.github.com/users/tangerzhang/orgs","repos_url":"https://api.github.com/users/tangerzhang/repos","events_url":"https://api.github.com/users/tangerzhang/events{/privacy}","received_events_url":"https://api.github.com/users/tangerzhang/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-04-24T05:04:00Z","updated_at":"2016-04-25T13:32:21Z","closed_at":null,"body":"Hello,\r\nI am using cormhap to correct Pacbio reads of a large genome and canu automatically assigned 1077 jobs in SLRUM system. However, the default MaxArraySize is 1001 in the SLRUM system and I do not have root permission to modify the config. Is it possible to change canu parameters to avoid this failure?\r\nAny suggestion is appreciate.\r\n"},"comment":{"url":"https://api.github.com/repos/marbl/canu/issues/comments/214329339","html_url":"https://github.com/marbl/canu/issues/114#issuecomment-214329339","issue_url":"https://api.github.com/repos/marbl/canu/issues/114","id":214329339,"user":{"login":"skoren","id":923478,"avatar_url":"https://avatars.githubusercontent.com/u/923478?v=3","gravatar_id":"","url":"https://api.github.com/users/skoren","html_url":"https://github.com/skoren","followers_url":"https://api.github.com/users/skoren/followers","following_url":"https://api.github.com/users/skoren/following{/other_user}","gists_url":"https://api.github.com/users/skoren/gists{/gist_id}","starred_url":"https://api.github.com/users/skoren/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/skoren/subscriptions","organizations_url":"https://api.github.com/users/skoren/orgs","repos_url":"https://api.github.com/users/skoren/repos","events_url":"https://api.github.com/users/skoren/events{/privacy}","received_events_url":"https://api.github.com/users/skoren/received_events","type":"User","site_admin":false},"created_at":"2016-04-25T13:32:21Z","updated_at":"2016-04-25T13:32:21Z","body":"You can increase the memory used for the overlapping steps. Doubling the limit it picked would work and will end up with half as many jobs. Assuming it picked 18gb, something like:\r\n```\r\ncormhapMemory=36 obtovlMemory=12 utgovlMemory=12g obtOvlHashBlockLength=200000000 utgOvlHashBlockLength=200000000\r\n```\r\nShould decrease the number of overlapping jobs by 2 on all steps, assuming you have more memory per machine."}}