{"action":"closed","issue":{"url":"https://api.github.com/repos/pachterlab/kallisto/issues/66","labels_url":"https://api.github.com/repos/pachterlab/kallisto/issues/66/labels{/name}","comments_url":"https://api.github.com/repos/pachterlab/kallisto/issues/66/comments","events_url":"https://api.github.com/repos/pachterlab/kallisto/issues/66/events","html_url":"https://github.com/pachterlab/kallisto/issues/66","id":98817191,"number":66,"title":"quant: unrecognized option '--pseudobam'","user":{"login":"moldach","id":5749465,"avatar_url":"https://avatars.githubusercontent.com/u/5749465?v=3","gravatar_id":"","url":"https://api.github.com/users/moldach","html_url":"https://github.com/moldach","followers_url":"https://api.github.com/users/moldach/followers","following_url":"https://api.github.com/users/moldach/following{/other_user}","gists_url":"https://api.github.com/users/moldach/gists{/gist_id}","starred_url":"https://api.github.com/users/moldach/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/moldach/subscriptions","organizations_url":"https://api.github.com/users/moldach/orgs","repos_url":"https://api.github.com/users/moldach/repos","events_url":"https://api.github.com/users/moldach/events{/privacy}","received_events_url":"https://api.github.com/users/moldach/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-08-03T19:03:00Z","updated_at":"2015-08-14T04:42:38Z","closed_at":"2015-08-14T04:42:38Z","body":" It is my understanding that we should only supply one sample at a time to kallisto; therefore I ran the following command on one of my 48 Single-end FASTQ files. However, I'm getting a strange error.\r\n \r\nAlthough 'quant' does produce three output files (abundance.h5, abundances.tsv, run_info.jso), I cannot understand why the --pseudobam command is not recognized (or executed) and why there is no SAM format output?\r\nHoping someone can help!\r\n ![troubleshoot](https://cloud.githubusercontent.com/assets/5749465/9045271/2be75880-39df-11e5-9eac-d0a6ad088289.jpg)\r\n"}}