{"action":"created","issue":{"url":"https://api.github.com/repos/ENCODE-DCC/long-rna-seq-pipeline/issues/1","labels_url":"https://api.github.com/repos/ENCODE-DCC/long-rna-seq-pipeline/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/ENCODE-DCC/long-rna-seq-pipeline/issues/1/comments","events_url":"https://api.github.com/repos/ENCODE-DCC/long-rna-seq-pipeline/issues/1/events","html_url":"https://github.com/ENCODE-DCC/long-rna-seq-pipeline/issues/1","id":90245664,"number":1,"title":"STAR Index from ENCFF483PAE uses sjdbGTFtagExonParentGene","user":{"login":"detrout","id":975038,"avatar_url":"https://avatars.githubusercontent.com/u/975038?v=3","gravatar_id":"","url":"https://api.github.com/users/detrout","html_url":"https://github.com/detrout","followers_url":"https://api.github.com/users/detrout/followers","following_url":"https://api.github.com/users/detrout/following{/other_user}","gists_url":"https://api.github.com/users/detrout/gists{/gist_id}","starred_url":"https://api.github.com/users/detrout/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/detrout/subscriptions","organizations_url":"https://api.github.com/users/detrout/orgs","repos_url":"https://api.github.com/users/detrout/repos","events_url":"https://api.github.com/users/detrout/events{/privacy}","received_events_url":"https://api.github.com/users/detrout/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-06-22T23:47:29Z","updated_at":"2015-06-23T18:00:42Z","closed_at":null,"body":"The version of STAR linked to from the git submodule does not support that parameter, the  sjdbGTFtagExonParentGene parameter appears to have been added in a later version of STAR. \r\n\r\nPerhaps the submodule needs to be updated?"},"comment":{"url":"https://api.github.com/repos/ENCODE-DCC/long-rna-seq-pipeline/issues/comments/114591452","html_url":"https://github.com/ENCODE-DCC/long-rna-seq-pipeline/issues/1#issuecomment-114591452","issue_url":"https://api.github.com/repos/ENCODE-DCC/long-rna-seq-pipeline/issues/1","id":114591452,"user":{"login":"detrout","id":975038,"avatar_url":"https://avatars.githubusercontent.com/u/975038?v=3","gravatar_id":"","url":"https://api.github.com/users/detrout","html_url":"https://github.com/detrout","followers_url":"https://api.github.com/users/detrout/followers","following_url":"https://api.github.com/users/detrout/following{/other_user}","gists_url":"https://api.github.com/users/detrout/gists{/gist_id}","starred_url":"https://api.github.com/users/detrout/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/detrout/subscriptions","organizations_url":"https://api.github.com/users/detrout/orgs","repos_url":"https://api.github.com/users/detrout/repos","events_url":"https://api.github.com/users/detrout/events{/privacy}","received_events_url":"https://api.github.com/users/detrout/received_events","type":"User","site_admin":false},"created_at":"2015-06-23T18:00:42Z","updated_at":"2015-06-23T18:00:42Z","body":"I asked Cricket if there was a place I could download the STAR & RSEM indexes from and she pointed me to https://www.encodeproject.org/search/?searchTerm=reference&type=dataset&lab.title=ENCODE%20Processing%20Pipeline I downloaded ENCFF064YNQ.tar.gz  ENCFF518RJA.tar.gz and ENCFF647OKF.tar.gz for the male & female STAR indexes and the RSEM index. \r\n\r\nI'm pretty sure the error message I got was from the version of STAR from this git repository when used against the index files I extracted from the accessions above.\r\n\r\nWhat accessions are you using for the indexes for dnanexus pipeline? It could be there's a newer index built that you're not actually using."}}