{"action":"created","issue":{"url":"https://api.github.com/repos/jodyphelan/TBProfiler/issues/3","repository_url":"https://api.github.com/repos/jodyphelan/TBProfiler","labels_url":"https://api.github.com/repos/jodyphelan/TBProfiler/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/jodyphelan/TBProfiler/issues/3/comments","events_url":"https://api.github.com/repos/jodyphelan/TBProfiler/issues/3/events","html_url":"https://github.com/jodyphelan/TBProfiler/issues/3","id":242025925,"number":3,"title":"When we run tb-profiler in ubuntu 14.04, we got exception","user":{"login":"yujun2017","id":25592652,"avatar_url":"https://avatars6.githubusercontent.com/u/25592652?v=4","gravatar_id":"","url":"https://api.github.com/users/yujun2017","html_url":"https://github.com/yujun2017","followers_url":"https://api.github.com/users/yujun2017/followers","following_url":"https://api.github.com/users/yujun2017/following{/other_user}","gists_url":"https://api.github.com/users/yujun2017/gists{/gist_id}","starred_url":"https://api.github.com/users/yujun2017/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yujun2017/subscriptions","organizations_url":"https://api.github.com/users/yujun2017/orgs","repos_url":"https://api.github.com/users/yujun2017/repos","events_url":"https://api.github.com/users/yujun2017/events{/privacy}","received_events_url":"https://api.github.com/users/yujun2017/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"jodyphelan","id":8697224,"avatar_url":"https://avatars5.githubusercontent.com/u/8697224?v=4","gravatar_id":"","url":"https://api.github.com/users/jodyphelan","html_url":"https://github.com/jodyphelan","followers_url":"https://api.github.com/users/jodyphelan/followers","following_url":"https://api.github.com/users/jodyphelan/following{/other_user}","gists_url":"https://api.github.com/users/jodyphelan/gists{/gist_id}","starred_url":"https://api.github.com/users/jodyphelan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jodyphelan/subscriptions","organizations_url":"https://api.github.com/users/jodyphelan/orgs","repos_url":"https://api.github.com/users/jodyphelan/repos","events_url":"https://api.github.com/users/jodyphelan/events{/privacy}","received_events_url":"https://api.github.com/users/jodyphelan/received_events","type":"User","site_admin":false},"assignees":[{"login":"jodyphelan","id":8697224,"avatar_url":"https://avatars5.githubusercontent.com/u/8697224?v=4","gravatar_id":"","url":"https://api.github.com/users/jodyphelan","html_url":"https://github.com/jodyphelan","followers_url":"https://api.github.com/users/jodyphelan/followers","following_url":"https://api.github.com/users/jodyphelan/following{/other_user}","gists_url":"https://api.github.com/users/jodyphelan/gists{/gist_id}","starred_url":"https://api.github.com/users/jodyphelan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jodyphelan/subscriptions","organizations_url":"https://api.github.com/users/jodyphelan/orgs","repos_url":"https://api.github.com/users/jodyphelan/repos","events_url":"https://api.github.com/users/jodyphelan/events{/privacy}","received_events_url":"https://api.github.com/users/jodyphelan/received_events","type":"User","site_admin":false}],"milestone":null,"comments":2,"created_at":"2017-07-11T12:13:16Z","updated_at":"2017-07-17T13:38:51Z","closed_at":null,"body":"When we run tb-profiler in Ubuntu v14.04, we got exception. The error message is:\r\nset([])\r\nTraceback (most recent call last):\r\n  File \"TBProfiler/tb-profiler\", line 538, in <module>\r\n    args.func(args)\r\n  File \"TBProfiler/tb-profiler\", line 500, in main_run_pipeline\r\n    lin = assign_lin(args.prefix)\r\n  File \"TBProfiler/tb-profiler\", line 91, in assign_lin\r\n    dict_sample_lin[sample_lin[0].split(\".\")[0]] = sorted([x for x in sample_lin if \".\" in x and sample_lin[0].split(\".\")[0] in x])[-1]\r\nIndexError: list index out of range\r\n\r\nit works fine in Mac machine using same sample files.\r\n\r\nBy the way, is it possible to use Bam files as input file instead of fastq file? It is too slow to use when we input fastq files. \r\n"},"comment":{"url":"https://api.github.com/repos/jodyphelan/TBProfiler/issues/comments/315758106","html_url":"https://github.com/jodyphelan/TBProfiler/issues/3#issuecomment-315758106","issue_url":"https://api.github.com/repos/jodyphelan/TBProfiler/issues/3","id":315758106,"user":{"login":"yujun2017","id":25592652,"avatar_url":"https://avatars6.githubusercontent.com/u/25592652?v=4","gravatar_id":"","url":"https://api.github.com/users/yujun2017","html_url":"https://github.com/yujun2017","followers_url":"https://api.github.com/users/yujun2017/followers","following_url":"https://api.github.com/users/yujun2017/following{/other_user}","gists_url":"https://api.github.com/users/yujun2017/gists{/gist_id}","starred_url":"https://api.github.com/users/yujun2017/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yujun2017/subscriptions","organizations_url":"https://api.github.com/users/yujun2017/orgs","repos_url":"https://api.github.com/users/yujun2017/repos","events_url":"https://api.github.com/users/yujun2017/events{/privacy}","received_events_url":"https://api.github.com/users/yujun2017/received_events","type":"User","site_admin":false},"created_at":"2017-07-17T13:38:51Z","updated_at":"2017-07-17T13:38:51Z","body":"Jody:\n   Thank you so much. I think this option will help us lot.\n   By the way, we do find a big problem when we are using TBProfiler. The\nsimple test is: using the same fastq file in Mac OS and Ubuntu, the result\nis different. This is why I got error when I am running same fastq file in\nUbuntu. Can you try to downsampling using seqtk to 100K or 200K to do test?\nYou will find result is different. I guess the SNAP filter is different.\n\nThank you so much!\n\nJun Yu\n\nOn 15 July 2017 at 04:36, jodyphelan <notifications@github.com> wrote:\n\n> Hi YuJun,\n>\n> I suspect that there is a difference in the way SNAP and BWA have created\n> the bams. I will look into this. Great idea to include a bam input option.\n> I will include this in the next release.\n>\n> Best,\n> Jody\n>\n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/jodyphelan/TBProfiler/issues/3#issuecomment-315519661>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AYaDTJD5oOZtM7YSXqh8OKUNw0KW7AA1ks5sOHnzgaJpZM4OUJIm>\n> .\n>\n\n\n\n-- \n\nJohn Yu\n"}}
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