{"action":"created","issue":{"url":"https://api.github.com/repos/biocore/qiime/issues/1830","labels_url":"https://api.github.com/repos/biocore/qiime/issues/1830/labels{/name}","comments_url":"https://api.github.com/repos/biocore/qiime/issues/1830/comments","events_url":"https://api.github.com/repos/biocore/qiime/issues/1830/events","html_url":"https://github.com/biocore/qiime/issues/1830","id":53765244,"number":1830,"title":"--minimum_failure_threshold not properly implemented","user":{"login":"mlangill","id":456888,"avatar_url":"https://avatars.githubusercontent.com/u/456888?v=3","gravatar_id":"","url":"https://api.github.com/users/mlangill","html_url":"https://github.com/mlangill","followers_url":"https://api.github.com/users/mlangill/followers","following_url":"https://api.github.com/users/mlangill/following{/other_user}","gists_url":"https://api.github.com/users/mlangill/gists{/gist_id}","starred_url":"https://api.github.com/users/mlangill/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mlangill/subscriptions","organizations_url":"https://api.github.com/users/mlangill/orgs","repos_url":"https://api.github.com/users/mlangill/repos","events_url":"https://api.github.com/users/mlangill/events{/privacy}","received_events_url":"https://api.github.com/users/mlangill/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/biocore/qiime/labels/bug","name":"bug","color":"e10c02"}],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/biocore/qiime/milestones/21","labels_url":"https://api.github.com/repos/biocore/qiime/milestones/21/labels","id":530599,"number":21,"title":"QIIME 1.9.0","description":"This will likely be the last minor release under QIIME 1. ","creator":{"login":"jairideout","id":1847232,"avatar_url":"https://avatars.githubusercontent.com/u/1847232?v=3","gravatar_id":"","url":"https://api.github.com/users/jairideout","html_url":"https://github.com/jairideout","followers_url":"https://api.github.com/users/jairideout/followers","following_url":"https://api.github.com/users/jairideout/following{/other_user}","gists_url":"https://api.github.com/users/jairideout/gists{/gist_id}","starred_url":"https://api.github.com/users/jairideout/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jairideout/subscriptions","organizations_url":"https://api.github.com/users/jairideout/orgs","repos_url":"https://api.github.com/users/jairideout/repos","events_url":"https://api.github.com/users/jairideout/events{/privacy}","received_events_url":"https://api.github.com/users/jairideout/received_events","type":"User","site_admin":false},"open_issues":22,"closed_issues":236,"state":"open","created_at":"2014-01-08T19:45:01Z","updated_at":"2015-01-08T16:25:45Z","due_on":"2014-12-19T07:00:00Z","closed_at":null},"comments":2,"created_at":"2015-01-08T15:52:50Z","updated_at":"2015-01-08T16:40:53Z","closed_at":null,"body":"Within the script pick_open_reference_otus.py the --minimum_failure_threshold is properly described in the documentation to decide whether or not to do steps 2 and 3 (or skip right to steps 4) by comparing this threshold (default being set to 100,000 which by the way is not included in the documentation) to the **number of sequences failing the reference picking step**. However, the threshold is improperly compared to the **number of subsampled sequences**. \r\n\r\nThis bug causes the pipeline to skip steps 2 and 3 when the defaults are used even with very large datasets (e.g. 5 million failed reads are attempted to be de novo otu picked in step 4). \r\n\r\nA PR will be issued shortly to address this. \r\n"},"comment":{"url":"https://api.github.com/repos/biocore/qiime/issues/comments/69207101","html_url":"https://github.com/biocore/qiime/issues/1830#issuecomment-69207101","issue_url":"https://api.github.com/repos/biocore/qiime/issues/1830","id":69207101,"user":{"login":"mlangill","id":456888,"avatar_url":"https://avatars.githubusercontent.com/u/456888?v=3","gravatar_id":"","url":"https://api.github.com/users/mlangill","html_url":"https://github.com/mlangill","followers_url":"https://api.github.com/users/mlangill/followers","following_url":"https://api.github.com/users/mlangill/following{/other_user}","gists_url":"https://api.github.com/users/mlangill/gists{/gist_id}","starred_url":"https://api.github.com/users/mlangill/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mlangill/subscriptions","organizations_url":"https://api.github.com/users/mlangill/orgs","repos_url":"https://api.github.com/users/mlangill/repos","events_url":"https://api.github.com/users/mlangill/events{/privacy}","received_events_url":"https://api.github.com/users/mlangill/received_events","type":"User","site_admin":false},"created_at":"2015-01-08T16:40:53Z","updated_at":"2015-01-08T16:40:53Z","body":"Yes, this was on QIIME 1.9.0-rc1. PR should be sent in about 5 minutes. "}}