{"action":"opened","issue":{"url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/100","repository_url":"https://api.github.com/repos/COMBINE-lab/salmon","labels_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/100/labels{/name}","comments_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/100/comments","events_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/100/events","html_url":"https://github.com/COMBINE-lab/salmon/issues/100","id":187377792,"number":100,"title":"Infinite indexing time?","user":{"login":"fruce-ki","id":18140986,"avatar_url":"https://avatars.githubusercontent.com/u/18140986?v=3","gravatar_id":"","url":"https://api.github.com/users/fruce-ki","html_url":"https://github.com/fruce-ki","followers_url":"https://api.github.com/users/fruce-ki/followers","following_url":"https://api.github.com/users/fruce-ki/following{/other_user}","gists_url":"https://api.github.com/users/fruce-ki/gists{/gist_id}","starred_url":"https://api.github.com/users/fruce-ki/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fruce-ki/subscriptions","organizations_url":"https://api.github.com/users/fruce-ki/orgs","repos_url":"https://api.github.com/users/fruce-ki/repos","events_url":"https://api.github.com/users/fruce-ki/events{/privacy}","received_events_url":"https://api.github.com/users/fruce-ki/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-11-04T16:23:49Z","updated_at":"2016-11-04T16:23:49Z","closed_at":null,"body":"I've been using 0.7.1 without problems until today.\r\nI'm trying to index the transcriptome (made with gffread) of human GRCh37 from archived Ensembl 60.\r\n\r\nThe process has been running for hours, with no messages beyond this:\r\n\r\n```\r\nVersion Info: ### A newer version of Salmon is available. ####\r\n###\r\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases \r\ncontains some new features and minor bug fixes; please upgrade at your\r\nearliest convenience.\r\n###\r\n[2016-11-04 13:45:38.583] [jLog] [info] building index\r\nRapMap Indexer\r\n\r\n[Step 1 of 4] : counting k-mers\r\n\r\n```\r\n\r\nThis is all there is in the index.log\r\n\r\n`[2016-11-04 13:45:38.583] [jLog] [info] building index`\r\n\r\nNone of me previous indexes have taken so long, especially not in total silence. So I'm guessing it gets stuck somewhere, but where? Why?\r\n\r\nI know there is a newer version, but getting our busy sysadmin to install things takes time and I didn;t see anything critical for my usage case listed in the release notes."}}
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