{"action":"created","issue":{"url":"https://api.github.com/repos/dnanexus/viral-ngs/issues/53","repository_url":"https://api.github.com/repos/dnanexus/viral-ngs","labels_url":"https://api.github.com/repos/dnanexus/viral-ngs/issues/53/labels{/name}","comments_url":"https://api.github.com/repos/dnanexus/viral-ngs/issues/53/comments","events_url":"https://api.github.com/repos/dnanexus/viral-ngs/issues/53/events","html_url":"https://github.com/dnanexus/viral-ngs/issues/53","id":180719700,"number":53,"title":"Enable bwa metagenomics by default","user":{"login":"yesimon","id":601839,"avatar_url":"https://avatars.githubusercontent.com/u/601839?v=3","gravatar_id":"","url":"https://api.github.com/users/yesimon","html_url":"https://github.com/yesimon","followers_url":"https://api.github.com/users/yesimon/followers","following_url":"https://api.github.com/users/yesimon/following{/other_user}","gists_url":"https://api.github.com/users/yesimon/gists{/gist_id}","starred_url":"https://api.github.com/users/yesimon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yesimon/subscriptions","organizations_url":"https://api.github.com/users/yesimon/orgs","repos_url":"https://api.github.com/users/yesimon/repos","events_url":"https://api.github.com/users/yesimon/events{/privacy}","received_events_url":"https://api.github.com/users/yesimon/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-10-03T19:04:48Z","updated_at":"2016-10-18T19:46:36Z","closed_at":null,"body":"The newly introduced bwa metagenomics step aligns against an index that requires a flat 8G memory. Runtime should be on par with a typical human bwa alignment. Due to the relatively high runtime we need to consider the instance types being targeted and whether it will be cost-effective."},"comment":{"url":"https://api.github.com/repos/dnanexus/viral-ngs/issues/comments/254618171","html_url":"https://github.com/dnanexus/viral-ngs/issues/53#issuecomment-254618171","issue_url":"https://api.github.com/repos/dnanexus/viral-ngs/issues/53","id":254618171,"user":{"login":"dpark01","id":8513746,"avatar_url":"https://avatars.githubusercontent.com/u/8513746?v=3","gravatar_id":"","url":"https://api.github.com/users/dpark01","html_url":"https://github.com/dpark01","followers_url":"https://api.github.com/users/dpark01/followers","following_url":"https://api.github.com/users/dpark01/following{/other_user}","gists_url":"https://api.github.com/users/dpark01/gists{/gist_id}","starred_url":"https://api.github.com/users/dpark01/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dpark01/subscriptions","organizations_url":"https://api.github.com/users/dpark01/orgs","repos_url":"https://api.github.com/users/dpark01/repos","events_url":"https://api.github.com/users/dpark01/events{/privacy}","received_events_url":"https://api.github.com/users/dpark01/received_events","type":"User","site_admin":false},"created_at":"2016-10-18T19:46:36Z","updated_at":"2016-10-18T19:46:36Z","body":"Yeah I think there's some more work to be done here on our end first--there's some validation work on the method itself, but also we'll want to write out the workflow and provide an equivalent db. Maybe after @tomkinsc gets a few more bits converted to WDL, we can propose a WDL for bwa-lca metagenomics as well. @yesimon when you say high runtime, how long are we talking (on, say, a c4.2xlarge or c3.2xlarge)?"}}
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