{"action":"created","issue":{"url":"https://api.github.com/repos/ekg/freebayes/issues/222","labels_url":"https://api.github.com/repos/ekg/freebayes/issues/222/labels{/name}","comments_url":"https://api.github.com/repos/ekg/freebayes/issues/222/comments","events_url":"https://api.github.com/repos/ekg/freebayes/issues/222/events","html_url":"https://github.com/ekg/freebayes/issues/222","id":117569412,"number":222,"title":"Memory issues with 14 000 WGS samples","user":{"login":"mfz","id":4185526,"avatar_url":"https://avatars.githubusercontent.com/u/4185526?v=3","gravatar_id":"","url":"https://api.github.com/users/mfz","html_url":"https://github.com/mfz","followers_url":"https://api.github.com/users/mfz/followers","following_url":"https://api.github.com/users/mfz/following{/other_user}","gists_url":"https://api.github.com/users/mfz/gists{/gist_id}","starred_url":"https://api.github.com/users/mfz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mfz/subscriptions","organizations_url":"https://api.github.com/users/mfz/orgs","repos_url":"https://api.github.com/users/mfz/repos","events_url":"https://api.github.com/users/mfz/events{/privacy}","received_events_url":"https://api.github.com/users/mfz/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-11-18T11:42:52Z","updated_at":"2015-12-15T15:06:05Z","closed_at":null,"body":"Hi everyone!\r\n\r\nWe are trying to call 14 000 WGS samples with an average depth of around 30, but are always running into memory problems.\r\n\r\nWe are running 2 processes on 64 Gb RAM, where each process receives a 5 kbp region to process, and set option --use-best-n-alleles=4.\r\n\r\nEither SLURM kills the process due to excessive memory usage,\r\nor freebayes exits with exit code 137 and simply prints 'Killed'.\r\n\r\nThe version of freebayes we are running is v1.0.0-19-gefe685d-dirty (previous versions showed the same behaviour).\r\n\r\nAny advice on parameter tuning etc. would be appreciated.\r\n\r\nBest regards,\r\nFlorian\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/ekg/freebayes/issues/comments/164791437","html_url":"https://github.com/ekg/freebayes/issues/222#issuecomment-164791437","issue_url":"https://api.github.com/repos/ekg/freebayes/issues/222","id":164791437,"user":{"login":"ekg","id":145425,"avatar_url":"https://avatars.githubusercontent.com/u/145425?v=3","gravatar_id":"","url":"https://api.github.com/users/ekg","html_url":"https://github.com/ekg","followers_url":"https://api.github.com/users/ekg/followers","following_url":"https://api.github.com/users/ekg/following{/other_user}","gists_url":"https://api.github.com/users/ekg/gists{/gist_id}","starred_url":"https://api.github.com/users/ekg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ekg/subscriptions","organizations_url":"https://api.github.com/users/ekg/orgs","repos_url":"https://api.github.com/users/ekg/repos","events_url":"https://api.github.com/users/ekg/events{/privacy}","received_events_url":"https://api.github.com/users/ekg/received_events","type":"User","site_admin":false},"created_at":"2015-12-15T15:06:05Z","updated_at":"2015-12-15T15:06:05Z","body":"16G is probably not enough. Do you have a system where you could get a\nsense for how much memory it needs? It might be >50G.\nOn Dec 15, 2015 1:35 AM, \"mfz\" <notifications@github.com> wrote:\n\n> Hi Erik,\n>\n> I did the testing using v1.0.1-1-g683b3cc with --use-best-nalleles 3,\n> using a chunk size of 5000 bp and 16 Gb of memory, but freebayes keeps\n> exiting with exit code 137.\n> Florian\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/ekg/freebayes/issues/222#issuecomment-164683360>.\n>\n"}}