{"action":"created","issue":{"url":"https://api.github.com/repos/heathsc/gemBS/issues/22","repository_url":"https://api.github.com/repos/heathsc/gemBS","labels_url":"https://api.github.com/repos/heathsc/gemBS/issues/22/labels{/name}","comments_url":"https://api.github.com/repos/heathsc/gemBS/issues/22/comments","events_url":"https://api.github.com/repos/heathsc/gemBS/issues/22/events","html_url":"https://github.com/heathsc/gemBS/issues/22","id":337410307,"node_id":"MDU6SXNzdWUzMzc0MTAzMDc=","number":22,"title":"gem-indexer error","user":{"login":"codyace","id":28378138,"node_id":"MDQ6VXNlcjI4Mzc4MTM4","avatar_url":"https://avatars2.githubusercontent.com/u/28378138?v=4","gravatar_id":"","url":"https://api.github.com/users/codyace","html_url":"https://github.com/codyace","followers_url":"https://api.github.com/users/codyace/followers","following_url":"https://api.github.com/users/codyace/following{/other_user}","gists_url":"https://api.github.com/users/codyace/gists{/gist_id}","starred_url":"https://api.github.com/users/codyace/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/codyace/subscriptions","organizations_url":"https://api.github.com/users/codyace/orgs","repos_url":"https://api.github.com/users/codyace/repos","events_url":"https://api.github.com/users/codyace/events{/privacy}","received_events_url":"https://api.github.com/users/codyace/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-07-02T08:06:45Z","updated_at":"2018-07-02T08:29:17Z","closed_at":null,"author_association":"NONE","body":"When follow the 14. Worked example in http://statgen.cnag.cat/gemBS/UserGuide/_build/html/example.html\r\n\r\n:\r\n: Command index started at 2018-07-02 16:06:22.354822\r\n:\r\n: Creating index\r\n2018-07-02 16:06:22,824 ERROR: Process '~/.local/lib/python3.6/site-packages/gemBS/gemBSbinaries/gem-indexer' finished with 1\r\n2018-07-02 16:06:22,825 ERROR: 2018/7/2 16:06:22 -- [Inspecting MultiFASTA]\r\n2018-07-02 16:06:22,825 ERROR: 2018/7/2 16:06:22 --  100% ... done [0.020 s]\r\n2018-07-02 16:06:22,825 ERROR: 2018/7/2 16:06:22 -- Inspected text 15268125 characters (index_complement=yes). Requesting 14 MB (encoded text)\r\n2018-07-02 16:06:22,825 ERROR: 2018/7/2 16:06:22 -- [Reading MultiFASTA]\r\n2018-07-02 16:06:22,825 ERROR: GEM::Error (archive_builder_text.c:225,archive_builder_text_generate_forward)\r\n2018-07-02 16:06:22,825 ERROR: MultiFASTA parsing (indexes/sacCer3.BS_gemBS.tmp.gz:1). must start with a tag '>'\r\nValueError: Error while executing the Bisulphite gem-indexer"},"comment":{"url":"https://api.github.com/repos/heathsc/gemBS/issues/comments/401710668","html_url":"https://github.com/heathsc/gemBS/issues/22#issuecomment-401710668","issue_url":"https://api.github.com/repos/heathsc/gemBS/issues/22","id":401710668,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMTcxMDY2OA==","user":{"login":"heathsc","id":3264375,"node_id":"MDQ6VXNlcjMyNjQzNzU=","avatar_url":"https://avatars2.githubusercontent.com/u/3264375?v=4","gravatar_id":"","url":"https://api.github.com/users/heathsc","html_url":"https://github.com/heathsc","followers_url":"https://api.github.com/users/heathsc/followers","following_url":"https://api.github.com/users/heathsc/following{/other_user}","gists_url":"https://api.github.com/users/heathsc/gists{/gist_id}","starred_url":"https://api.github.com/users/heathsc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/heathsc/subscriptions","organizations_url":"https://api.github.com/users/heathsc/orgs","repos_url":"https://api.github.com/users/heathsc/repos","events_url":"https://api.github.com/users/heathsc/events{/privacy}","received_events_url":"https://api.github.com/users/heathsc/received_events","type":"User","site_admin":false},"created_at":"2018-07-02T08:29:17Z","updated_at":"2018-07-02T08:29:17Z","author_association":"OWNER","body":"Thank you for the bug report.  Could you run the command:\n\ngemBS --loglevel debug index\n\nand send the output?  Do you have pigz installed?  If pigz is missing this might lead to this behaviour (we should report an error in this instance and/or fall back to use gzip).\n\nCheers,\nSimon\n\n\n> On 2 Jul 2018, at 10:06, codyace <notifications@github.com> wrote:\n> \n> When follow the 14. Worked example in http://statgen.cnag.cat/gemBS/UserGuide/_build/html/example.html <http://statgen.cnag.cat/gemBS/UserGuide/_build/html/example.html>\n> :\n> : Command index started at 2018-07-02 16:06:22.354822\n> :\n> : Creating index\n> 2018-07-02 16:06:22,824 ERROR: Process '~/.local/lib/python3.6/site-packages/gemBS/gemBSbinaries/gem-indexer' finished with 1\n> 2018-07-02 16:06:22,825 ERROR: 2018/7/2 16:06:22 -- [Inspecting MultiFASTA]\n> 2018-07-02 16:06:22,825 ERROR: 2018/7/2 16:06:22 -- 100% ... done [0.020 s]\n> 2018-07-02 16:06:22,825 ERROR: 2018/7/2 16:06:22 -- Inspected text 15268125 characters (index_complement=yes). Requesting 14 MB (encoded text)\n> 2018-07-02 16:06:22,825 ERROR: 2018/7/2 16:06:22 -- [Reading MultiFASTA]\n> 2018-07-02 16:06:22,825 ERROR: GEM::Error (archive_builder_text.c:225,archive_builder_text_generate_forward)\n> 2018-07-02 16:06:22,825 ERROR: MultiFASTA parsing (indexes/sacCer3.BS_gemBS.tmp.gz:1). must start with a tag '>'\n> ValueError: Error while executing the Bisulphite gem-indexer\n> \n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub <https://github.com/heathsc/gemBS/issues/22>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADHPd7A6f5IWnqdlZTYY8dx5hplhp3ERks5uCdSVgaJpZM4U-3L7>.\n> \n\n"}}
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