{"action":"created","issue":{"url":"https://api.github.com/repos/stschiff/msmc2/issues/3","repository_url":"https://api.github.com/repos/stschiff/msmc2","labels_url":"https://api.github.com/repos/stschiff/msmc2/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/stschiff/msmc2/issues/3/comments","events_url":"https://api.github.com/repos/stschiff/msmc2/issues/3/events","html_url":"https://github.com/stschiff/msmc2/issues/3","id":145691709,"number":3,"title":"Excessive memory usage","user":{"login":"feilchenfeldt","id":4295843,"avatar_url":"https://avatars.githubusercontent.com/u/4295843?v=3","gravatar_id":"","url":"https://api.github.com/users/feilchenfeldt","html_url":"https://github.com/feilchenfeldt","followers_url":"https://api.github.com/users/feilchenfeldt/followers","following_url":"https://api.github.com/users/feilchenfeldt/following{/other_user}","gists_url":"https://api.github.com/users/feilchenfeldt/gists{/gist_id}","starred_url":"https://api.github.com/users/feilchenfeldt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/feilchenfeldt/subscriptions","organizations_url":"https://api.github.com/users/feilchenfeldt/orgs","repos_url":"https://api.github.com/users/feilchenfeldt/repos","events_url":"https://api.github.com/users/feilchenfeldt/events{/privacy}","received_events_url":"https://api.github.com/users/feilchenfeldt/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-04-04T14:00:29Z","updated_at":"2016-07-21T14:43:30Z","closed_at":null,"body":"Hi Stephan,\r\n\r\nWhen I am running msmc2 in sep mode on 4 haplotypes I often run in memory issues with the program getting killed by our compute cluster because it is using more than 250gb of memory at the first Baumwelch iteration. The genomes are the size of human genomes but with more variation.\r\n\r\nIs there a way to restrict memory usage? I played a bit with reducing the number of cpus used, could that help?\r\n\r\nMany thanks,\r\nHannes"},"comment":{"url":"https://api.github.com/repos/stschiff/msmc2/issues/comments/234275675","html_url":"https://github.com/stschiff/msmc2/issues/3#issuecomment-234275675","issue_url":"https://api.github.com/repos/stschiff/msmc2/issues/3","id":234275675,"user":{"login":"biozzq","id":15704257,"avatar_url":"https://avatars.githubusercontent.com/u/15704257?v=3","gravatar_id":"","url":"https://api.github.com/users/biozzq","html_url":"https://github.com/biozzq","followers_url":"https://api.github.com/users/biozzq/followers","following_url":"https://api.github.com/users/biozzq/following{/other_user}","gists_url":"https://api.github.com/users/biozzq/gists{/gist_id}","starred_url":"https://api.github.com/users/biozzq/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/biozzq/subscriptions","organizations_url":"https://api.github.com/users/biozzq/orgs","repos_url":"https://api.github.com/users/biozzq/repos","events_url":"https://api.github.com/users/biozzq/events{/privacy}","received_events_url":"https://api.github.com/users/biozzq/received_events","type":"User","site_admin":false},"created_at":"2016-07-21T14:43:30Z","updated_at":"2016-07-21T14:43:30Z","body":"Hi Stephan,\r\n\r\nThe file contains 29 chromosomes, I have merge them in one file using `cat`. Is this the cause of the excessive memory usage ? \r\n\r\nmany thanks"}}
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