{"action":"closed","issue":{"url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/269","repository_url":"https://api.github.com/repos/broadinstitute/viral-ngs","labels_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/269/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/269/comments","events_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/269/events","html_url":"https://github.com/broadinstitute/viral-ngs/issues/269","id":149947498,"number":269,"title":"kraken gzipped reads output file errors","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},"labels":[],"state":"closed","locked":false,"assignee":{"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},"milestone":null,"comments":0,"created_at":"2016-04-21T03:00:07Z","updated_at":"2016-04-22T01:46:11Z","closed_at":"2016-04-22T01:46:11Z","body":"Bug: if --outReport specified, [metagenomics.kraken](https://github.com/broadinstitute/viral-ngs/blob/master/metagenomics.py#L51) runs kraken-report on \"outReads\" as input. This may not exist (if --outReads is None) and even if it does, it is likely gzipped, which kraken-report won't like. Perhaps it should take \"tmp_filtered_reads\" as input?\r\n\r\nDesire: can the [opening of outReport](https://github.com/broadinstitute/viral-ngs/blob/master/metagenomics.py#L47) be changed to use util.file.open_or_gzopen instead? Might be nice to allow people to write out uncompressed .txt or compressed .txt.gz files depending on the output filename.\r\n"}}