{"action":"created","issue":{"url":"https://api.github.com/repos/jade-cheng/ohana/issues/5","repository_url":"https://api.github.com/repos/jade-cheng/ohana","labels_url":"https://api.github.com/repos/jade-cheng/ohana/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/jade-cheng/ohana/issues/5/comments","events_url":"https://api.github.com/repos/jade-cheng/ohana/issues/5/events","html_url":"https://github.com/jade-cheng/ohana/issues/5","id":294278447,"number":5,"title":"convert crashing","user":{"login":"yassineS","id":1767457,"avatar_url":"https://avatars1.githubusercontent.com/u/1767457?v=4","gravatar_id":"","url":"https://api.github.com/users/yassineS","html_url":"https://github.com/yassineS","followers_url":"https://api.github.com/users/yassineS/followers","following_url":"https://api.github.com/users/yassineS/following{/other_user}","gists_url":"https://api.github.com/users/yassineS/gists{/gist_id}","starred_url":"https://api.github.com/users/yassineS/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yassineS/subscriptions","organizations_url":"https://api.github.com/users/yassineS/orgs","repos_url":"https://api.github.com/users/yassineS/repos","events_url":"https://api.github.com/users/yassineS/events{/privacy}","received_events_url":"https://api.github.com/users/yassineS/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-02-05T05:32:28Z","updated_at":"2018-02-06T03:36:10Z","closed_at":null,"author_association":"NONE","body":"Hi Jade,\r\n\r\nI keep running into an issue with convert. I am trying to convert a likelihood file in beagle format into lgm format without luck. The file contains 70-odd samples. I keep getting the following error:\r\n\r\n```\r\nconvert bgl2lgm input.bgl output.lgm\r\nstd::bad_alloc\r\n```\r\n\r\nNote that I'm running this on a machine with 32 cores and 240GB of ram, so I don't think it's a memory issue as there's more memory available than the uncompressed data file size.\r\n\r\nThanks,\r\nYassine"},"comment":{"url":"https://api.github.com/repos/jade-cheng/ohana/issues/comments/363300490","html_url":"https://github.com/jade-cheng/ohana/issues/5#issuecomment-363300490","issue_url":"https://api.github.com/repos/jade-cheng/ohana/issues/5","id":363300490,"user":{"login":"yassineS","id":1767457,"avatar_url":"https://avatars1.githubusercontent.com/u/1767457?v=4","gravatar_id":"","url":"https://api.github.com/users/yassineS","html_url":"https://github.com/yassineS","followers_url":"https://api.github.com/users/yassineS/followers","following_url":"https://api.github.com/users/yassineS/following{/other_user}","gists_url":"https://api.github.com/users/yassineS/gists{/gist_id}","starred_url":"https://api.github.com/users/yassineS/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yassineS/subscriptions","organizations_url":"https://api.github.com/users/yassineS/orgs","repos_url":"https://api.github.com/users/yassineS/repos","events_url":"https://api.github.com/users/yassineS/events{/privacy}","received_events_url":"https://api.github.com/users/yassineS/received_events","type":"User","site_admin":false},"created_at":"2018-02-06T03:36:09Z","updated_at":"2018-02-06T03:36:09Z","author_association":"NONE","body":"Hi Jade,\n\nIt works fine for the snippet but not the full dataset. That’s my issue, it crashes complaining about memory hence: `std::bad_alloc`.\n\nY\n\n> On 6 Feb 2018, at 2:04 pm, Jade Cheng <notifications@github.com <mailto:notifications@github.com>> wrote:\n> \n> This snippet of data seems to work fine for me (copied below). Could you give it a try?\n> \n> $ cat input.bgl \n> marker\tallele1\tallele2\tInd0\tInd0\tInd0\tInd1\tInd1\tInd1\n> 1_14930\t0\t2\t0.333333\t0.333333\t0.333333\t0.005268\t0.331576\t0.663157\n> 1_14933\t2\t0\t0.333333\t0.333333\t0.333333\t0.666633\t0.333314\t0.000053\n> 1_17462\t2\t0\t0.333333\t0.333333\t0.333333\t0.666633\t0.333314\t0.000053\n> 1_20131\t2\t0\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\n> 1_51914\t3\t0\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\n> 1_51935\t1\t0\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\n> 1_51954\t2\t0\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\n> 1_54652\t0\t1\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\n> 1_54669\t1\t0\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\n> \n> $ convert bgl2lgm input.bgl output.lgm\n> \n> $ cat output.lgm \n> 2 9\n> 0.333333\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\n> 0.005268\t0.666633\t0.666633\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\n> \n> 2 9\n> 0.333333\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\n> 0.331576\t0.333314\t0.333314\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\n> \n> 2 9\n> 0.333333\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\n> 0.663157\t5.3e-05\t5.3e-05\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\t0.333333\n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub <https://github.com/jade-cheng/ohana/issues/5#issuecomment-363300203>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABr4IYJWNc0OQvGMbsAOSHPnHHSEt9qRks5tR8hAgaJpZM4R48HA>.\n> \n\n"}}
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