{"action":"opened","issue":{"url":"https://api.github.com/repos/YangLab/CIRCexplorer/issues/7","labels_url":"https://api.github.com/repos/YangLab/CIRCexplorer/issues/7/labels{/name}","comments_url":"https://api.github.com/repos/YangLab/CIRCexplorer/issues/7/comments","events_url":"https://api.github.com/repos/YangLab/CIRCexplorer/issues/7/events","html_url":"https://github.com/YangLab/CIRCexplorer/issues/7","id":89069074,"number":7,"title":"Issue running CIRCexplorer","user":{"login":"madmblac","id":12939540,"avatar_url":"https://avatars.githubusercontent.com/u/12939540?v=3","gravatar_id":"","url":"https://api.github.com/users/madmblac","html_url":"https://github.com/madmblac","followers_url":"https://api.github.com/users/madmblac/followers","following_url":"https://api.github.com/users/madmblac/following{/other_user}","gists_url":"https://api.github.com/users/madmblac/gists{/gist_id}","starred_url":"https://api.github.com/users/madmblac/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/madmblac/subscriptions","organizations_url":"https://api.github.com/users/madmblac/orgs","repos_url":"https://api.github.com/users/madmblac/repos","events_url":"https://api.github.com/users/madmblac/events{/privacy}","received_events_url":"https://api.github.com/users/madmblac/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-06-17T16:50:43Z","updated_at":"2015-06-17T16:50:43Z","closed_at":null,"body":"I am trying to use CIRCexplorer with STAR mapper and the error \"IndexError: list index out of range\" keeps occurring. I can't figure out how to remedy this problem, any help would be appreciated. Here is my command line: \r\n  python CIRCexplorer.py -j 0002-surg-funsion-junction.txt --genome=human.hg19.genome --ref=UCSC_Refseq_sno_miRNA_lncipedia_3_0_hg19_11-10-2014.gtf \r\n\r\nStart CIRCexplorer 1.1.1\r\nStart to annotate fusion junctions...\r\nTraceback (most recent call last):\r\n  File \"CIRCexplorer.py\", line 494, in <module>\r\n    annotate_fusion(ref_f, temp1, temp2)\r\n  File \"CIRCexplorer.py\", line 67, in annotate_fusion\r\n    genes, gene_info = parse_ref1(ref_f)  # gene annotations\r\n  File \"CIRCexplorer.py\", line 201, in parse_ref1\r\n    start = starts[0]\r\nIndexError: list index out of range"}}