{"action":"created","issue":{"url":"https://api.github.com/repos/voutcn/megahit/issues/27","labels_url":"https://api.github.com/repos/voutcn/megahit/issues/27/labels{/name}","comments_url":"https://api.github.com/repos/voutcn/megahit/issues/27/comments","events_url":"https://api.github.com/repos/voutcn/megahit/issues/27/events","html_url":"https://github.com/voutcn/megahit/issues/27","id":60508807,"number":27,"title":"Insufficient memory warning","user":{"login":"shaman-narayanasamy","id":4169854,"avatar_url":"https://avatars.githubusercontent.com/u/4169854?v=3","gravatar_id":"","url":"https://api.github.com/users/shaman-narayanasamy","html_url":"https://github.com/shaman-narayanasamy","followers_url":"https://api.github.com/users/shaman-narayanasamy/followers","following_url":"https://api.github.com/users/shaman-narayanasamy/following{/other_user}","gists_url":"https://api.github.com/users/shaman-narayanasamy/gists{/gist_id}","starred_url":"https://api.github.com/users/shaman-narayanasamy/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/shaman-narayanasamy/subscriptions","organizations_url":"https://api.github.com/users/shaman-narayanasamy/orgs","repos_url":"https://api.github.com/users/shaman-narayanasamy/repos","events_url":"https://api.github.com/users/shaman-narayanasamy/events{/privacy}","received_events_url":"https://api.github.com/users/shaman-narayanasamy/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-03-10T14:35:31Z","updated_at":"2015-03-10T15:19:40Z","closed_at":null,"body":"I receive a flurry of these warnings over and over again in the terminal:\r\n\r\n```\r\n[B::ReadInputFile WRANING] No enough memory to hold all the reads. Only the first 37292817 reads are kept.\r\n```\r\n\r\nIs this supposed to happen? FYI, I am using the \"long read\" bug fixed version."},"comment":{"url":"https://api.github.com/repos/voutcn/megahit/issues/comments/78076025","html_url":"https://github.com/voutcn/megahit/issues/27#issuecomment-78076025","issue_url":"https://api.github.com/repos/voutcn/megahit/issues/27","id":78076025,"user":{"login":"voutcn","id":6329785,"avatar_url":"https://avatars.githubusercontent.com/u/6329785?v=3","gravatar_id":"","url":"https://api.github.com/users/voutcn","html_url":"https://github.com/voutcn","followers_url":"https://api.github.com/users/voutcn/followers","following_url":"https://api.github.com/users/voutcn/following{/other_user}","gists_url":"https://api.github.com/users/voutcn/gists{/gist_id}","starred_url":"https://api.github.com/users/voutcn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/voutcn/subscriptions","organizations_url":"https://api.github.com/users/voutcn/orgs","repos_url":"https://api.github.com/users/voutcn/repos","events_url":"https://api.github.com/users/voutcn/events{/privacy}","received_events_url":"https://api.github.com/users/voutcn/received_events","type":"User","site_admin":false},"created_at":"2015-03-10T15:19:40Z","updated_at":"2015-03-10T15:19:40Z","body":"I guess that you set a very large `-l` parameter.\r\nMEGAHIT will load all reads into memory before graph construction. It uses fixed length (max read length specified by `-l`) to store reads, so when `-l` is large, it needs more memory for the reads.\r\n\r\nAnd the waring message is explained on [this wiki page](https://github.com/voutcn/megahit/wiki/MEGAHIT-Memory-setting):\r\n>When the memory specified by -m is not enough to hold all reads, MEGAHIT will raise a warning message and try to keep only a portion of reads and perform a partial assembly. "}}