{"action":"opened","issue":{"url":"https://api.github.com/repos/nextgenusfs/funannotate/issues/160","repository_url":"https://api.github.com/repos/nextgenusfs/funannotate","labels_url":"https://api.github.com/repos/nextgenusfs/funannotate/issues/160/labels{/name}","comments_url":"https://api.github.com/repos/nextgenusfs/funannotate/issues/160/comments","events_url":"https://api.github.com/repos/nextgenusfs/funannotate/issues/160/events","html_url":"https://github.com/nextgenusfs/funannotate/issues/160","id":308866978,"number":160,"title":"strain level phylogeny","user":{"login":"AnotherSimon","id":36060453,"avatar_url":"https://avatars1.githubusercontent.com/u/36060453?v=4","gravatar_id":"","url":"https://api.github.com/users/AnotherSimon","html_url":"https://github.com/AnotherSimon","followers_url":"https://api.github.com/users/AnotherSimon/followers","following_url":"https://api.github.com/users/AnotherSimon/following{/other_user}","gists_url":"https://api.github.com/users/AnotherSimon/gists{/gist_id}","starred_url":"https://api.github.com/users/AnotherSimon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AnotherSimon/subscriptions","organizations_url":"https://api.github.com/users/AnotherSimon/orgs","repos_url":"https://api.github.com/users/AnotherSimon/repos","events_url":"https://api.github.com/users/AnotherSimon/events{/privacy}","received_events_url":"https://api.github.com/users/AnotherSimon/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-03-27T08:19:44Z","updated_at":"2018-03-27T08:19:44Z","closed_at":null,"author_association":"NONE","body":"For my current project I'm working on a comparison of various strains within the same species. I used the `--strain` option for each of the genomes to be compared.\r\n\r\nWhen running `funannotate compare` most of the outputs are unusable because the naming stops at the species level and I suspect it is also messing with some of the output files due to their naming scheme (for example: `./WorkingDir/funannotate_compare/go_terms/Genus_species.txt`)"}}
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