{"action":"opened","issue":{"url":"https://api.github.com/repos/lindaszabo/KNIFE/issues/5","repository_url":"https://api.github.com/repos/lindaszabo/KNIFE","labels_url":"https://api.github.com/repos/lindaszabo/KNIFE/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/lindaszabo/KNIFE/issues/5/comments","events_url":"https://api.github.com/repos/lindaszabo/KNIFE/issues/5/events","html_url":"https://github.com/lindaszabo/KNIFE/issues/5","id":191381867,"number":5,"title":"Error in predictJunctions GLM while running KNIFE","user":{"login":"ShobanaSekar","id":11082964,"avatar_url":"https://avatars.githubusercontent.com/u/11082964?v=3","gravatar_id":"","url":"https://api.github.com/users/ShobanaSekar","html_url":"https://github.com/ShobanaSekar","followers_url":"https://api.github.com/users/ShobanaSekar/followers","following_url":"https://api.github.com/users/ShobanaSekar/following{/other_user}","gists_url":"https://api.github.com/users/ShobanaSekar/gists{/gist_id}","starred_url":"https://api.github.com/users/ShobanaSekar/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ShobanaSekar/subscriptions","organizations_url":"https://api.github.com/users/ShobanaSekar/orgs","repos_url":"https://api.github.com/users/ShobanaSekar/repos","events_url":"https://api.github.com/users/ShobanaSekar/events{/privacy}","received_events_url":"https://api.github.com/users/ShobanaSekar/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-11-23T21:18:24Z","updated_at":"2016-11-23T21:18:24Z","closed_at":null,"body":"Hi,\r\n\r\nI am trying to run KNIFE_v1.4 on some of our samples and am running into a few errors for some of them. I am getting these during the call to predictJunctions_tableData.r\r\n\r\n**Error 1:**\r\n\r\nError in rbindlist(list(linear_reads, decoy_reads)) : Item 2 has 7 columns, inconsistent with item 1 which has 6 columns. If instead you need to fill missing columns, use set argument 'fill' to TRUE.\r\nExecution halted\r\n\r\n\r\n**Error 2 (for a different sample):**\r\n\r\nError in fread(classFile, header = TRUE, sep = \"\\t\") :\r\n  File '/scratch/ssekar/circRNA/fastqs_n_tools/ADCC/KNIFE/ADCC_0019_PC_Whole_C1_OV2TD_L02544.proj/ADCC_0019_PC_Whole_C1_OV2TD_L02544.proj/circReads/ids/ADCC_0019_PC_Whole_C1_OV2TD_L02544.proj_R1__output.txt' does not exist. Include one or more spaces to consider the input a system command.\r\n\r\nThe file fread() complains to be missing is actually present and not empty. I am not sure what else is causing this error. This is all going through fine for 15/20 samples I am running this on. \r\n\r\nIt will be really helpful to get your inputs on fixing these errors.\r\n\r\nThank you,\r\nShobana Sekar"}}
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