{"action":"created","issue":{"url":"https://api.github.com/repos/pachterlab/kallisto/issues/76","labels_url":"https://api.github.com/repos/pachterlab/kallisto/issues/76/labels{/name}","comments_url":"https://api.github.com/repos/pachterlab/kallisto/issues/76/comments","events_url":"https://api.github.com/repos/pachterlab/kallisto/issues/76/events","html_url":"https://github.com/pachterlab/kallisto/issues/76","id":103003325,"number":76,"title":"TPM is “-nan”","user":{"login":"flying-sheep","id":291575,"avatar_url":"https://avatars.githubusercontent.com/u/291575?v=3","gravatar_id":"","url":"https://api.github.com/users/flying-sheep","html_url":"https://github.com/flying-sheep","followers_url":"https://api.github.com/users/flying-sheep/followers","following_url":"https://api.github.com/users/flying-sheep/following{/other_user}","gists_url":"https://api.github.com/users/flying-sheep/gists{/gist_id}","starred_url":"https://api.github.com/users/flying-sheep/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/flying-sheep/subscriptions","organizations_url":"https://api.github.com/users/flying-sheep/orgs","repos_url":"https://api.github.com/users/flying-sheep/repos","events_url":"https://api.github.com/users/flying-sheep/events{/privacy}","received_events_url":"https://api.github.com/users/flying-sheep/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":10,"created_at":"2015-08-25T11:34:35Z","updated_at":"2015-08-26T05:58:15Z","closed_at":"2015-08-26T02:13:53Z","body":"Hi, running the following command with [this reference](http://bio.math.berkeley.edu/kallisto/transcriptomes/Mus_musculus.GRCm38.rel79.cdna.all.fa.gz) index and [this file](https://gist.github.com/flying-sheep/6462174f840b990c138e)\r\n\r\n`kallisto quant -i Mus_musculus.GRCm38.rel79.cdna.all.fa.idx -o CAAAG --single -l 100 CAAAG_1.fastq.gz`\r\n\r\nresults in a abundances.tsv like this:\r\n\r\n```tab\r\ntarget_id\tlength\teff_length\test_counts\ttpm\r\nENSMUST00000178537\t12\t12\t0\t-nan\r\nENSMUST00000178862\t14\t14\t0\t-nan\r\nENSMUST00000177564\t16\t16\t0\t-nan\r\nENSMUST00000179664\t11\t11\t0\t-nan\r\nENSMUST00000179883\t16\t16\t0\t-nan\r\n...\r\n```\r\n\r\nis there anything wrong with the input or is this a bug?"},"comment":{"url":"https://api.github.com/repos/pachterlab/kallisto/issues/comments/134845762","html_url":"https://github.com/pachterlab/kallisto/issues/76#issuecomment-134845762","issue_url":"https://api.github.com/repos/pachterlab/kallisto/issues/76","id":134845762,"user":{"login":"flying-sheep","id":291575,"avatar_url":"https://avatars.githubusercontent.com/u/291575?v=3","gravatar_id":"","url":"https://api.github.com/users/flying-sheep","html_url":"https://github.com/flying-sheep","followers_url":"https://api.github.com/users/flying-sheep/followers","following_url":"https://api.github.com/users/flying-sheep/following{/other_user}","gists_url":"https://api.github.com/users/flying-sheep/gists{/gist_id}","starred_url":"https://api.github.com/users/flying-sheep/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/flying-sheep/subscriptions","organizations_url":"https://api.github.com/users/flying-sheep/orgs","repos_url":"https://api.github.com/users/flying-sheep/repos","events_url":"https://api.github.com/users/flying-sheep/events{/privacy}","received_events_url":"https://api.github.com/users/flying-sheep/received_events","type":"User","site_admin":false},"created_at":"2015-08-26T05:58:15Z","updated_at":"2015-08-26T05:58:15Z","body":"Thanks!\r\n\r\nOne question for clarification: Why do you not do the exit status thing now but consider it for the future? What changes in the future?"}}