{"action":"created","issue":{"url":"https://api.github.com/repos/GMOD/jbrowse/issues/1113","repository_url":"https://api.github.com/repos/GMOD/jbrowse","labels_url":"https://api.github.com/repos/GMOD/jbrowse/issues/1113/labels{/name}","comments_url":"https://api.github.com/repos/GMOD/jbrowse/issues/1113/comments","events_url":"https://api.github.com/repos/GMOD/jbrowse/issues/1113/events","html_url":"https://github.com/GMOD/jbrowse/issues/1113","id":340733497,"node_id":"MDU6SXNzdWUzNDA3MzM0OTc=","number":1113,"title":"generate-names.pl memory usage on large VCF track","user":{"login":"garrett-stevens","id":25592344,"node_id":"MDQ6VXNlcjI1NTkyMzQ0","avatar_url":"https://avatars0.githubusercontent.com/u/25592344?v=4","gravatar_id":"","url":"https://api.github.com/users/garrett-stevens","html_url":"https://github.com/garrett-stevens","followers_url":"https://api.github.com/users/garrett-stevens/followers","following_url":"https://api.github.com/users/garrett-stevens/following{/other_user}","gists_url":"https://api.github.com/users/garrett-stevens/gists{/gist_id}","starred_url":"https://api.github.com/users/garrett-stevens/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/garrett-stevens/subscriptions","organizations_url":"https://api.github.com/users/garrett-stevens/orgs","repos_url":"https://api.github.com/users/garrett-stevens/repos","events_url":"https://api.github.com/users/garrett-stevens/events{/privacy}","received_events_url":"https://api.github.com/users/garrett-stevens/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-07-12T17:40:33Z","updated_at":"2018-07-12T19:54:32Z","closed_at":"2018-07-12T18:59:14Z","author_association":"NONE","body":"Hello there,\r\n\r\nI'm trying to use `generate-names.pl` with an (admittedly huge) VCF track, but it keeps freezing up my machine due to using up all available memory. My track looks like this:\r\n```json\r\n{\r\n  \"label\":\"dbSNP\",\r\n  \"trackType\":null,\r\n  \"urlTemplate\":\"extra/dbsnp_20180423.vcf.gz\",\r\n  \"storeClass\":\"JBrowse/Store/SeqFeature/VCFTabix\",\r\n  \"category\":\"Annotations\",\r\n  \"key\":\"dbSNP\",\r\n  \"type\":\"CanvasVariants\"\r\n}\r\n```\r\nAnd the VCF is the dbSNP VCF pulled straight from NCBI (`ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/VCF/All_20180423.vcf.gz` and accompanying `.tbi`), about 14.6 GB. I'm running the command without specifying any memory limits:\r\n```\r\nbin/generate-names.pl --tracks dbSNP\r\n```\r\nI've tried this on a cloud machine with 244 GB of memory (AWS r4.8xlarge if you're interested) and it still ran out of memory. I'm not sure if this is a bug or just beyond the scope of what `generate-names.pl` was intended to be used for.\r\n\r\nThanks!\r\n\r\nEDIT: I'm using the latest version (1.14.2) of JBrowse."},"comment":{"url":"https://api.github.com/repos/GMOD/jbrowse/issues/comments/404631198","html_url":"https://github.com/GMOD/jbrowse/issues/1113#issuecomment-404631198","issue_url":"https://api.github.com/repos/GMOD/jbrowse/issues/1113","id":404631198,"node_id":"MDEyOklzc3VlQ29tbWVudDQwNDYzMTE5OA==","user":{"login":"cmdcolin","id":6511937,"node_id":"MDQ6VXNlcjY1MTE5Mzc=","avatar_url":"https://avatars0.githubusercontent.com/u/6511937?v=4","gravatar_id":"","url":"https://api.github.com/users/cmdcolin","html_url":"https://github.com/cmdcolin","followers_url":"https://api.github.com/users/cmdcolin/followers","following_url":"https://api.github.com/users/cmdcolin/following{/other_user}","gists_url":"https://api.github.com/users/cmdcolin/gists{/gist_id}","starred_url":"https://api.github.com/users/cmdcolin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmdcolin/subscriptions","organizations_url":"https://api.github.com/users/cmdcolin/orgs","repos_url":"https://api.github.com/users/cmdcolin/repos","events_url":"https://api.github.com/users/cmdcolin/events{/privacy}","received_events_url":"https://api.github.com/users/cmdcolin/received_events","type":"User","site_admin":false},"created_at":"2018-07-12T19:54:32Z","updated_at":"2018-07-12T19:54:32Z","author_association":"CONTRIBUTOR","body":"Didn't mean to close the issue but I guess hopefully it can be closed given the workaround :)"}}
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