{"action":"created","issue":{"url":"https://api.github.com/repos/vgteam/vg/issues/267","repository_url":"https://api.github.com/repos/vgteam/vg","labels_url":"https://api.github.com/repos/vgteam/vg/issues/267/labels{/name}","comments_url":"https://api.github.com/repos/vgteam/vg/issues/267/comments","events_url":"https://api.github.com/repos/vgteam/vg/issues/267/events","html_url":"https://github.com/vgteam/vg/issues/267","id":141690503,"number":267,"title":"vg index: xg construction memory usage increase ","user":{"login":"mlin","id":356550,"avatar_url":"https://avatars.githubusercontent.com/u/356550?v=3","gravatar_id":"","url":"https://api.github.com/users/mlin","html_url":"https://github.com/mlin","followers_url":"https://api.github.com/users/mlin/followers","following_url":"https://api.github.com/users/mlin/following{/other_user}","gists_url":"https://api.github.com/users/mlin/gists{/gist_id}","starred_url":"https://api.github.com/users/mlin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mlin/subscriptions","organizations_url":"https://api.github.com/users/mlin/orgs","repos_url":"https://api.github.com/users/mlin/repos","events_url":"https://api.github.com/users/mlin/events{/privacy}","received_events_url":"https://api.github.com/users/mlin/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":22,"created_at":"2016-03-17T19:54:20Z","updated_at":"2016-03-30T13:42:31Z","closed_at":"2016-03-30T12:33:24Z","body":"I'm noticing memory usage in `vg index` to build the xg index has increased quite a lot in the last few weeks. Previously and for a long time, this operation maxed out at roughly 200 GiB of RAM on the whole-genome 1000G graph. Now I see it blowing through the machine's 244 GiB. Is this expected, anything to be done?\r\n\r\n(Edited to remove misleading reference to gcsa2)\r\n(Edited to remove misleading reference to 435c97c)"},"comment":{"url":"https://api.github.com/repos/vgteam/vg/issues/comments/203439283","html_url":"https://github.com/vgteam/vg/issues/267#issuecomment-203439283","issue_url":"https://api.github.com/repos/vgteam/vg/issues/267","id":203439283,"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":"2016-03-30T13:42:31Z","updated_at":"2016-03-30T13:42:31Z","body":"What is the pruning on this?\n\nOn Wed, Mar 30, 2016, 13:33 Mike Lin <notifications@github.com> wrote:\n\n> Looking GOOD! Mem usage for xg stayed <170GiB for the 1000G graph.\n> build_gcsa <60GiB.\n>\n> I am still using the old recipe\n> <https://github.com/vgteam/vg/wiki/working-with-a-whole-genome-variation-graph#xggcsa-index-high-memory-build-low-memory-runtime-fast>\n> to prepare the graph for build_gcsa (exact code\n> <https://github.com/dnanexus-rnd/dxvg/blob/xg/applets/vg_index/src/code.sh#L17>)\n> -- LMK when there's a new one!\n>\n> —\n> You are receiving this because you modified the open/close state.\n> Reply to this email directly or view it on GitHub\n> <https://github.com/vgteam/vg/issues/267#issuecomment-203409013>\n>\n"}}