{"action":"created","issue":{"url":"https://api.github.com/repos/Illumina/manta/issues/40","repository_url":"https://api.github.com/repos/Illumina/manta","labels_url":"https://api.github.com/repos/Illumina/manta/issues/40/labels{/name}","comments_url":"https://api.github.com/repos/Illumina/manta/issues/40/comments","events_url":"https://api.github.com/repos/Illumina/manta/issues/40/events","html_url":"https://github.com/Illumina/manta/issues/40","id":164687387,"number":40,"title":"manta error in running test data demo","user":{"login":"XiongLuoxing","id":16487161,"avatar_url":"https://avatars.githubusercontent.com/u/16487161?v=3","gravatar_id":"","url":"https://api.github.com/users/XiongLuoxing","html_url":"https://github.com/XiongLuoxing","followers_url":"https://api.github.com/users/XiongLuoxing/followers","following_url":"https://api.github.com/users/XiongLuoxing/following{/other_user}","gists_url":"https://api.github.com/users/XiongLuoxing/gists{/gist_id}","starred_url":"https://api.github.com/users/XiongLuoxing/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/XiongLuoxing/subscriptions","organizations_url":"https://api.github.com/users/XiongLuoxing/orgs","repos_url":"https://api.github.com/users/XiongLuoxing/repos","events_url":"https://api.github.com/users/XiongLuoxing/events{/privacy}","received_events_url":"https://api.github.com/users/XiongLuoxing/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-07-09T21:53:25Z","updated_at":"2016-07-11T00:35:39Z","closed_at":null,"body":"Dear manta teams:\r\n\r\nIt is a great pleasure that you have a so well-behaved structural variation calling platform.\r\n\r\nI'm trying to use manta. But running demo meets problem. I really want to use your program properly. And sincerely hope that you can give me some advice on how to debug. Really need your help.\r\n\r\nThe installation seems all right by \r\nmanta-0.29.6.release_src.tar.bz2.\r\n\r\nMy linux version is:\r\nLinux mgt.cluster.com 2.6.32-220.13.1.el6.x86_64 #1 SMP Tue Apr 17 23:56:34 BST 2012 x86_64 x86_64 x86_64 GNU/Linux\r\ngcc 4.8.5\r\npython 2.7.12\r\n\r\nThe installation is the same as:\r\n    wget https://github.com/Illumina/manta/releases/download/v${MANTA_VERSION}/manta-${MANTA_VERSION}.release_src.tar.bz2\r\n    tar -xjf manta-${MANTA_VERSION}.release_src.tar.bz2\r\n    mkdir build && cd build\r\n    # Ensure that CC and CXX are updated to target compiler if needed, e.g.:\r\n    #     export CC=/path/to/cc\r\n    #     export CXX=/path/to/c++\r\n    ../manta-${MANTA_VERSION}.release_src/configure --jobs=4 --prefix=/path/to/install\r\n    make -j4 install\r\n\r\nAnd while running \r\nrunMantaWorkflowDemo.py \r\nin the installation path, the error part of log is like this:\r\n\r\n[2016-07-09T21:44:08.978098] [mgt.cluster.com] [3563_1] [TaskManager] [ERROR] Failed to complete command task: 'getAlignmentStats_generateStats_000' launched from master workflow, error code: 1, command: '/Share/BP/xionglx/tools/manta-0.29.6-build/libexec/GetAlignmentStats --output-file /Share/BP/xionglx/tools/manta-0.29.6-build/bin/MantaDemoAnalysis/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /Share/BP/xionglx/tools/manta-0.29.6-build/share/demo/manta/data/HCC1954.NORMAL.30x.compare.COST16011_region.bam'\r\n[2016-07-09T21:44:08.991474] [mgt.cluster.com] [3563_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Error Message:\r\n[2016-07-09T21:44:08.994892] [mgt.cluster.com] [3563_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Last 6 stderr lines from task (of 6 total lines):\r\n[2016-07-09T21:44:08.994892] [mgt.cluster.com] [3563_1] [TaskManager] [ERROR] [2016-07-09T21:44:08.904889] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] FATAL_ERROR: EXCEPTION: locale::facet::_S_create_c_locale name not valid\r\n[2016-07-09T21:44:08.994892] [mgt.cluster.com] [3563_1] [TaskManager] [ERROR] [2016-07-09T21:44:08.911776] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] ...caught in program.run()\r\n[2016-07-09T21:44:08.994892] [mgt.cluster.com] [3563_1] [TaskManager] [ERROR] [2016-07-09T21:44:08.913878] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] cmdline: /Share/BP/xionglx/tools/manta-0.29.6-build/libexec/GetAlignmentStats --output-file /Share/BP/xionglx/tools/manta-0.29.6-build/bin/MantaDemoAnalysis/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /Share/BP/xionglx/tools/manta-0.29.6-build/share/demo/manta/data/HCC1954.NORMAL.30x.compare.COST16011_region.bam\r\n[2016-07-09T21:44:08.994892] [mgt.cluster.com] [3563_1] [TaskManager] [ERROR] [2016-07-09T21:44:08.915710] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] version:\t0.29.6\r\n[2016-07-09T21:44:08.994892] [mgt.cluster.com] [3563_1] [TaskManager] [ERROR] [2016-07-09T21:44:08.917367] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] buildTime:\t2016-07-09T21:25:51.900217Z\r\n[2016-07-09T21:44:08.994892] [mgt.cluster.com] [3563_1] [TaskManager] [ERROR] [2016-07-09T21:44:08.919056] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] compiler:\tg++-4.8.5\r\n[2016-07-09T21:44:08.998084] [mgt.cluster.com] [3563_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.\r\n[2016-07-09T21:44:14.596202] [mgt.cluster.com] [3563_1] [WorkflowRunner] [ERROR] Worklow terminated due to the following task errors:\r\n[2016-07-09T21:44:14.602155] [mgt.cluster.com] [3563_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getAlignmentStats_generateStats_000' launched from master workflow, error code: 1, command: '/Share/BP/xionglx/tools/manta-0.29.6-build/libexec/GetAlignmentStats --output-file /Share/BP/xionglx/tools/manta-0.29.6-build/bin/MantaDemoAnalysis/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /Share/BP/xionglx/tools/manta-0.29.6-build/share/demo/manta/data/HCC1954.NORMAL.30x.compare.COST16011_region.bam'\r\n[2016-07-09T21:44:14.606530] [mgt.cluster.com] [3563_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_000] Error Message:\r\n[2016-07-09T21:44:14.610924] [mgt.cluster.com] [3563_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_000] Last 6 stderr lines from task (of 6 total lines):\r\n[2016-07-09T21:44:14.610924] [mgt.cluster.com] [3563_1] [WorkflowRunner] [ERROR] [2016-07-09T21:44:08.904889] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] FATAL_ERROR: EXCEPTION: locale::facet::_S_create_c_locale name not valid\r\n[2016-07-09T21:44:14.610924] [mgt.cluster.com] [3563_1] [WorkflowRunner] [ERROR] [2016-07-09T21:44:08.911776] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] ...caught in program.run()\r\n[2016-07-09T21:44:14.610924] [mgt.cluster.com] [3563_1] [WorkflowRunner] [ERROR] [2016-07-09T21:44:08.913878] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] cmdline: /Share/BP/xionglx/tools/manta-0.29.6-build/libexec/GetAlignmentStats --output-file /Share/BP/xionglx/tools/manta-0.29.6-build/bin/MantaDemoAnalysis/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /Share/BP/xionglx/tools/manta-0.29.6-build/share/demo/manta/data/HCC1954.NORMAL.30x.compare.COST16011_region.bam\r\n[2016-07-09T21:44:14.610924] [mgt.cluster.com] [3563_1] [WorkflowRunner] [ERROR] [2016-07-09T21:44:08.915710] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] version:\t0.29.6\r\n[2016-07-09T21:44:14.610924] [mgt.cluster.com] [3563_1] [WorkflowRunner] [ERROR] [2016-07-09T21:44:08.917367] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] buildTime:\t2016-07-09T21:25:51.900217Z\r\n[2016-07-09T21:44:14.610924] [mgt.cluster.com] [3563_1] [WorkflowRunner] [ERROR] [2016-07-09T21:44:08.919056] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] compiler:\tg++-4.8.5\r\n\r\n\r\nLooking forward to your reply.\r\n\r\nBest,\r\nLuoxing."},"comment":{"url":"https://api.github.com/repos/Illumina/manta/issues/comments/231620566","html_url":"https://github.com/Illumina/manta/issues/40#issuecomment-231620566","issue_url":"https://api.github.com/repos/Illumina/manta/issues/40","id":231620566,"user":{"login":"XiongLuoxing","id":16487161,"avatar_url":"https://avatars.githubusercontent.com/u/16487161?v=3","gravatar_id":"","url":"https://api.github.com/users/XiongLuoxing","html_url":"https://github.com/XiongLuoxing","followers_url":"https://api.github.com/users/XiongLuoxing/followers","following_url":"https://api.github.com/users/XiongLuoxing/following{/other_user}","gists_url":"https://api.github.com/users/XiongLuoxing/gists{/gist_id}","starred_url":"https://api.github.com/users/XiongLuoxing/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/XiongLuoxing/subscriptions","organizations_url":"https://api.github.com/users/XiongLuoxing/orgs","repos_url":"https://api.github.com/users/XiongLuoxing/repos","events_url":"https://api.github.com/users/XiongLuoxing/events{/privacy}","received_events_url":"https://api.github.com/users/XiongLuoxing/received_events","type":"User","site_admin":false},"created_at":"2016-07-11T00:35:39Z","updated_at":"2016-07-11T00:35:39Z","body":"Thank you very much.\r\n\r\nI have reset LC_CTYPE while running ./runMantaWorkflowDemo.py like this:\r\nLC_CTYPE=\"en_US.UTF8\" ./runMantaWorkflowDemo.py \r\n\r\nThus LC_CTYPE is consistent with other LC_* values, and demo could be successfully run with last lines of log like this:\r\n\r\n[2016-07-11T00:32:27.347072] [mgt.cluster.com] [1787_1] [WorkflowRunner] Manta workflow successfully completed.\r\n[2016-07-11T00:32:27.347072] [mgt.cluster.com] [1787_1] [WorkflowRunner] \r\n[2016-07-11T00:32:27.347072] [mgt.cluster.com] [1787_1] [WorkflowRunner] \tworkflow version: 0.29.6\r\n[2016-07-11T00:32:27.349953] [mgt.cluster.com] [1787_1] [WorkflowRunner] \r\n[2016-07-11T00:32:27.352067] [mgt.cluster.com] [1787_1] [WorkflowRunner] Workflow successfully completed all tasks\r\n[2016-07-11T00:32:27.354336] [mgt.cluster.com] [1787_1] [WorkflowRunner] Elapsed time for full workflow: 5 sec\r\n\r\n**** Completed demo workflow execution.\r\n\r\n\r\n**** Starting comparison to expected results.\r\n**** Expected results dir: '/Share/BP/xionglx/tools/manta-0.29.6-build/share/demo/manta/expectedResults'\r\n**** Demo results dir: 'MantaDemoAnalysis/results/variants'\r\n\r\n\r\n**** No differences between expected and computed results.\r\n\r\n\r\n**** Demo/verification successfully completed\r\n\r\n\r\n\r\nI will try if resetting LC_CTYPE can make thing work for my own data.\r\n\r\nThank you again!!!\r\n\r\nBest,\r\nLuoxing"}}
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