{"action":"opened","issue":{"url":"https://api.github.com/repos/PacificBiosciences/SMRT-Analysis/issues/247","labels_url":"https://api.github.com/repos/PacificBiosciences/SMRT-Analysis/issues/247/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/SMRT-Analysis/issues/247/comments","events_url":"https://api.github.com/repos/PacificBiosciences/SMRT-Analysis/issues/247/events","html_url":"https://github.com/PacificBiosciences/SMRT-Analysis/issues/247","id":128526198,"number":247,"title":"Exiting smrtpipe last error: SmrtExit task://016437/P_Filter/filter_003of003 Failed ","user":{"login":"mixer997","id":16820652,"avatar_url":"https://avatars.githubusercontent.com/u/16820652?v=3","gravatar_id":"","url":"https://api.github.com/users/mixer997","html_url":"https://github.com/mixer997","followers_url":"https://api.github.com/users/mixer997/followers","following_url":"https://api.github.com/users/mixer997/following{/other_user}","gists_url":"https://api.github.com/users/mixer997/gists{/gist_id}","starred_url":"https://api.github.com/users/mixer997/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mixer997/subscriptions","organizations_url":"https://api.github.com/users/mixer997/orgs","repos_url":"https://api.github.com/users/mixer997/repos","events_url":"https://api.github.com/users/mixer997/events{/privacy}","received_events_url":"https://api.github.com/users/mixer997/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-01-25T12:27:57Z","updated_at":"2016-01-25T12:27:57Z","closed_at":null,"body":"Hello, \r\n\r\nI've installed the newest version of the smrt-analysis, applied all of the patches and configure to run on a cluster with pbs. I've follwed the example from http://www.pacb.com/wp-content/uploads/2015/09/SMRT-Analysis-Software-Installation-v2.3.0.pdf \"verify the installation\" and got such error:\r\n\"Exiting smrtpipe last error: SmrtExit task://016437/P_Filter/filter_003of003 Failed\"\r\nPlease check overviewRpt.log below.\r\nAny idea what could be wrong?\r\n\r\n---\r\nRegards,\r\nMixer\r\n\r\n\r\n# Writing stdout and stderr from Popen:\r\n[INFO] 2016-01-21 15:23:38,148 [__main__ <module> 287] Running /opt/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/bin/qsw_py.py version 1.0\r\n[DEBUG] 2016-01-21 15:23:38,148 [__main__ __parseArgs 83] Parsing args ['/opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.sh', '-S', '/bin/bash', '-V', '-q', 'standard', '-N', 'Fove016437', '-o', '/opt/smrtanalysis/userdata/jobs/016/016437/log/P_Fetch/overviewRpt.log', '-e', '/opt/smrtanalysis/userdata/jobs/016/016437/log/P_Fetch/overviewRpt.log', '-l', 'nodes=1:ppn=1', '-PBS']\r\n[DEBUG] 2016-01-21 15:23:38,150 [__main__ _writeWrapperScript 141] Completed writing wrapper script to /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit\r\n[INFO] 2016-01-21 15:23:38,150 [__main__ run 253] calling cmd : runjmsenv qsub -S /bin/bash -V -q standard -N Fove016437 -o /opt/smrtanalysis/userdata/jobs/016/016437/log/P_Fetch/overviewRpt.log -e /opt/smrtanalysis/userdata/jobs/016/016437/log/P_Fetch/overviewRpt.log -l nodes=1:ppn=1 /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.wrap.sh\r\n[INFO] 2016-01-21 15:23:38,513 [__main__ _waitForJobTermination 149] waiting for jobId 3181153 to complete\r\n[DEBUG] 2016-01-21 15:23:38,514 [__main__ _waitForJobTermination 162] calling cmd runjmsenv qstat 3181153\r\n[DEBUG] 2016-01-21 15:23:38,679 [__main__ _waitForJobTermination 181] Job id                    Name             User            Time Use S Queue\r\n------------------------- ---------------- --------------- -------- - -----\r\n3181153.creamce           Fove016437       smrtanalysis           0 Q standard       \r\n\r\n[DEBUG] 2016-01-21 15:23:43,682 [__main__ _waitForJobTermination 162] calling cmd runjmsenv qstat 3181153\r\n[DEBUG] 2016-01-21 15:23:43,790 [__main__ _waitForJobTermination 181] Job id                    Name             User            Time Use S Queue\r\n------------------------- ---------------- --------------- -------- - -----\r\n3181153.creamce           Fove016437       smrtanalysis           0 R standard       \r\n\r\n[DEBUG] 2016-01-21 15:23:48,794 [__main__ _waitForJobTermination 162] calling cmd runjmsenv qstat 3181153\r\n[DEBUG] 2016-01-21 15:23:48,902 [__main__ _waitForJobTermination 181] Job id                    Name             User            Time Use S Queue\r\n------------------------- ---------------- --------------- -------- - -----\r\n3181153.creamce           Fove016437       smrtanalysis           0 R standard       \r\n\r\n[DEBUG] 2016-01-21 15:23:53,906 [__main__ _waitForJobTermination 162] calling cmd runjmsenv qstat 3181153\r\n[DEBUG] 2016-01-21 15:23:54,025 [__main__ _waitForJobTermination 181] Job id                    Name             User            Time Use S Queue\r\n------------------------- ---------------- --------------- -------- - -----\r\n3181153.creamce           Fove016437       smrtanalysis           0 R standard       \r\n\r\n[DEBUG] 2016-01-21 15:23:59,030 [__main__ _waitForJobTermination 162] calling cmd runjmsenv qstat 3181153\r\n[DEBUG] 2016-01-21 15:23:59,205 [__main__ _waitForJobTermination 181] Job id                    Name             User            Time Use S Queue\r\n------------------------- ---------------- --------------- -------- - -----\r\n3181153.creamce           Fove016437       smrtanalysis    00:00:00 E standard       \r\n\r\n[DEBUG] 2016-01-21 15:24:04,210 [__main__ _waitForJobTermination 162] calling cmd runjmsenv qstat 3181153\r\n[WARNING] 2016-01-21 15:24:04,379 [__main__ _waitForJobTermination 175] qstat: Unknown Job Id 3181153.creamce.host\r\n\r\nqstat: Unknown Job Id 3181153.creamce.host\r\n\r\n[DEBUG] 2016-01-21 15:24:04,379 [__main__ _waitForJobTermination 181] \r\n[INFO] 2016-01-21 15:24:04,379 [__main__ _waitForJobTermination 194] Breaking. Found returncode 153\r\n[INFO] 2016-01-21 15:24:04,380 [__main__ _waitForJobTermination 200] Completed waiting for termination of jobId 3181153\r\n[DEBUG] 2016-01-21 15:24:04,380 [__main__ _extractExitCode 210] extracting exit code from /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit\r\nAttempt 1 still waiting for /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit. Got error [Errno 2] No such file or directory: '/opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit'. runtime 1.90734863281e-06\r\nAttempt 2 still waiting for /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit. Got error [Errno 2] No such file or directory: '/opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit'. runtime 5.0059261322\r\nAttempt 3 still waiting for /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit. Got error [Errno 2] No such file or directory: '/opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit'. runtime 10.0099320412\r\nAttempt 4 still waiting for /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit. Got error [Errno 2] No such file or directory: '/opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit'. runtime 15.0138671398\r\nAttempt 5 still waiting for /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit. Got error [Errno 2] No such file or directory: '/opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit'. runtime 20.0196840763\r\nAttempt 6 still waiting for /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit. Got error [Errno 2] No such file or directory: '/opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit'. runtime 25.0259130001\r\nAttempt 7 still waiting for /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit. Got error [Errno 2] No such file or directory: '/opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit'. runtime 30.0320501328\r\nAttempt 8 still waiting for /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit. Got error [Errno 2] No such file or directory: '/opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit'. runtime 35.0382790565\r\nAttempt 9 still waiting for /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit. Got error [Errno 2] No such file or directory: '/opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit'. runtime 40.0443100929\r\nAttempt 10 still waiting for /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit. Got error [Errno 2] No such file or directory: '/opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit'. runtime 45.0500049591\r\nAttempt 11 still waiting for /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit. Got error [Errno 2] No such file or directory: '/opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit'. runtime 50.0562460423\r\nAttempt 12 still waiting for /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit. Got error [Errno 2] No such file or directory: '/opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit'. runtime 55.0623989105\r\nAttempt 13 still waiting for /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit. Got error [Errno 2] No such file or directory: '/opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit'. runtime 60.0685179234\r\nAttempt 14 still waiting for /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit. Got error [Errno 2] No such file or directory: '/opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit'. runtime 65.0755109787\r\nAttempt 15 still waiting for /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit. Got error [Errno 2] No such file or directory: '/opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit'. runtime 70.0817739964\r\nAttempt 16 still waiting for /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit. Got error [Errno 2] No such file or directory: '/opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit'. runtime 75.0880069733\r\nAttempt 17 still waiting for /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit. Got error [Errno 2] No such file or directory: '/opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit'. runtime 80.0939941406\r\nAttempt 18 still waiting for /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit. Got error [Errno 2] No such file or directory: '/opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit'. runtime 85.0999751091\r\nAttempt 19 still waiting for /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit. Got error [Errno 2] No such file or directory: '/opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit'. runtime 90.1063649654\r\nTraceback (most recent call last):\r\n  File \"/opt/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/bin/qsw_py.py\", line 289, in <module>\r\n    sys.exit(app.run())\r\n  File \"/opt/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/bin/qsw_py.py\", line 267, in run\r\n    exitCode = self._extractExitCode(exitCodePath)\r\n  File \"/opt/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/bin/qsw_py.py\", line 239, in _extractExitCode\r\n    raise QSubError(\"Unable to extract exit code from file {f}\".format(f=fileName))\r\n__main__.QSubError: Unable to extract exit code from file /opt/smrtanalysis/userdata/jobs/016/016437/workflow/P_Fetch/overviewRpt.exit\r\n\r\n\r\n\r\n\r\n\r\n"}}