{"action":"opened","issue":{"url":"https://api.github.com/repos/sanger-pathogens/Roary/issues/288","repository_url":"https://api.github.com/repos/sanger-pathogens/Roary","labels_url":"https://api.github.com/repos/sanger-pathogens/Roary/issues/288/labels{/name}","comments_url":"https://api.github.com/repos/sanger-pathogens/Roary/issues/288/comments","events_url":"https://api.github.com/repos/sanger-pathogens/Roary/issues/288/events","html_url":"https://github.com/sanger-pathogens/Roary/issues/288","id":185994798,"number":288,"title":"Missing proteins in roary output","user":{"login":"thackl","id":9363087,"avatar_url":"https://avatars.githubusercontent.com/u/9363087?v=3","gravatar_id":"","url":"https://api.github.com/users/thackl","html_url":"https://github.com/thackl","followers_url":"https://api.github.com/users/thackl/followers","following_url":"https://api.github.com/users/thackl/following{/other_user}","gists_url":"https://api.github.com/users/thackl/gists{/gist_id}","starred_url":"https://api.github.com/users/thackl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/thackl/subscriptions","organizations_url":"https://api.github.com/users/thackl/orgs","repos_url":"https://api.github.com/users/thackl/repos","events_url":"https://api.github.com/users/thackl/events{/privacy}","received_events_url":"https://api.github.com/users/thackl/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-10-28T18:51:09Z","updated_at":"2016-10-28T18:51:09Z","closed_at":null,"body":"Hi,\r\n\r\nI am running roary (3.6.2) on a set of ~200 Prochlorococcus genomes. I annotated the genomes with Prokka, and did get 326414 proteins. However, when I run roary on the gffs, clustered_proteins only contains 320796 protein ids, i.e. 5618 proteins are missing from the final clusters. \r\n\r\nThe missing proteins are from different genomes, most of them are short, but not all. So far, I couldn't figure out a clear pattern.. Any idea, where/why the proteins might get lost?\r\n"}}
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