[INFO] 2016-08-16 18:15:02,481 Successfully found 3 files in xml:/PHShome/ry077/bin/smrtanalysis/userdata/jobs/016/016450/input.xml
[INFO] 2016-08-16 18:15:03,420 smrtpipe.py running on rgs11.research.partners.org
[INFO] 2016-08-16 18:15:03,420 SMRT Analysis 2.3.0 / SMRTpipe 1.87.139483
[INFO] 2016-08-16 18:15:06,325 Process id 34938
[INFO] 2016-08-16 18:15:13,228 Starting task://016450/P_Fetch/toFofn
[INFO] 2016-08-16 18:15:13,247 task P_Fetch.toFofn successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 0 slots.
[INFO] 2016-08-16 18:15:13,248 Workflow Completion Status 1/74 in (            1%) tasks completed.
[INFO] 2016-08-16 18:15:18,255 Starting task://016450/P_Fetch/overviewRpt
[INFO] 2016-08-16 18:15:18,255 Starting task://016450/P_Filter/filter.plsFofn.Scatter
[INFO] 2016-08-16 18:15:18,255 Starting task://016450/P_Fetch/adapterRpt
[INFO] 2016-08-16 18:15:18,274 task P_Filter.filter.plsFofn.Scatter successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 2 slots.
[INFO] 2016-08-16 18:15:18,275 Workflow Completion Status 2/74 in (            2%) tasks completed.
[INFO] 2016-08-16 18:15:23,286 Starting task://016450/P_Filter/filter_002of003
[INFO] 2016-08-16 18:15:23,286 Starting task://016450/P_Filter/filter_001of003
[INFO] 2016-08-16 18:15:23,287 Starting task://016450/P_Filter/filter_003of003
[INFO] 2016-08-16 18:15:49,485 task P_Fetch.overviewRpt successfully completed (12.00 sec (0.20 min)). freed 1 slots, using 7 slots.
[INFO] 2016-08-16 18:15:49,486 Workflow Completion Status 3/74 in (            4%) tasks completed.
[INFO] 2016-08-16 18:16:10,670 task P_Fetch.adapterRpt successfully completed (36.00 sec (0.60 min)). freed 1 slots, using 6 slots.
[INFO] 2016-08-16 18:16:10,671 Workflow Completion Status 4/74 in (            5%) tasks completed.
[INFO] 2016-08-16 18:17:38,341 task P_Filter.filter_002of003 successfully completed (57.00 sec (0.95 min)). freed 2 slots, using 4 slots.
[INFO] 2016-08-16 18:17:38,341 Workflow Completion Status 5/74 in (            6%) tasks completed.
[INFO] 2016-08-16 18:17:43,348 Starting task://016450/P_Filter/subreads_002of003
[INFO] 2016-08-16 18:18:24,784 task P_Filter.filter_001of003 successfully completed (38.00 sec (0.63 min)). freed 2 slots, using 3 slots.
[INFO] 2016-08-16 18:18:24,784 Workflow Completion Status 6/74 in (            8%) tasks completed.
[INFO] 2016-08-16 18:18:29,791 Starting task://016450/P_Filter/subreads_001of003
[INFO] 2016-08-16 18:19:09,840 task P_Filter.subreads_002of003 successfully completed (75.00 sec (1.25 min)). freed 1 slots, using 3 slots.
[INFO] 2016-08-16 18:19:09,841 Workflow Completion Status 7/74 in (            9%) tasks completed.
[INFO] 2016-08-16 18:19:26,255 task P_Filter.filter_003of003 successfully completed (129.00 sec (2.15 min)). freed 2 slots, using 1 slots.
[INFO] 2016-08-16 18:19:26,255 Workflow Completion Status 8/74 in (         . 10%) tasks completed.
[INFO] 2016-08-16 18:19:31,264 Starting task://016450/P_Filter/filter.summary.Gather
[INFO] 2016-08-16 18:19:31,264 Starting task://016450/P_Filter/subreads_003of003
[INFO] 2016-08-16 18:19:31,265 Starting task://016450/P_Filter/filter.rgnFofn.Gather
[INFO] 2016-08-16 18:19:31,285 task P_Filter.filter.rgnFofn.Gather successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 3 slots.
[INFO] 2016-08-16 18:19:31,285 Workflow Completion Status 9/74 in (         . 12%) tasks completed.
[INFO] 2016-08-16 18:19:36,292 Starting task://016450/P_Filter/subreadSummary
[INFO] 2016-08-16 18:19:37,463 task P_Filter.filter.summary.Gather successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 3 slots.
[INFO] 2016-08-16 18:19:37,464 Workflow Completion Status 10/74 in (         . 13%) tasks completed.
[INFO] 2016-08-16 18:19:42,468 Starting task://016450/P_FilterReports/statsRpt
[INFO] 2016-08-16 18:19:42,468 Starting task://016450/P_FilterReports/loadingRpt
[INFO] 2016-08-16 18:20:12,508 task P_Filter.subreads_001of003 successfully completed (83.00 sec (1.38 min)). freed 1 slots, using 4 slots.
[INFO] 2016-08-16 18:20:12,508 Workflow Completion Status 11/74 in (         . 14%) tasks completed.
[INFO] 2016-08-16 18:20:55,198 task P_FilterReports.loadingRpt successfully completed (10.00 sec (0.17 min)). freed 1 slots, using 3 slots.
[INFO] 2016-08-16 18:20:55,198 Workflow Completion Status 12/74 in (         . 16%) tasks completed.
[INFO] 2016-08-16 18:21:38,054 task P_Filter.subreadSummary successfully completed (58.00 sec (0.97 min)). freed 1 slots, using 2 slots.
[INFO] 2016-08-16 18:21:38,054 Workflow Completion Status 13/74 in (         . 17%) tasks completed.
[INFO] 2016-08-16 18:21:43,062 Starting task://016450/P_FilterReports/subreadRpt
[INFO] 2016-08-16 18:21:59,259 task P_FilterReports.statsRpt successfully completed (14.00 sec (0.23 min)). freed 1 slots, using 2 slots.
[INFO] 2016-08-16 18:21:59,259 Workflow Completion Status 14/74 in (         . 18%) tasks completed.
[INFO] 2016-08-16 18:22:00,412 task P_FilterReports.subreadRpt successfully completed (9.00 sec (0.15 min)). freed 1 slots, using 1 slots.
[INFO] 2016-08-16 18:22:00,412 Workflow Completion Status 15/74 in (        .. 20%) tasks completed.
[INFO] 2016-08-16 18:22:46,911 task P_Filter.subreads_003of003 successfully completed (130.00 sec (2.17 min)). freed 1 slots, using 0 slots.
[INFO] 2016-08-16 18:22:46,911 Workflow Completion Status 16/74 in (        .. 21%) tasks completed.
[INFO] 2016-08-16 18:22:51,918 Starting task://016450/P_Filter/subreads.subreadFastq.Gather
[INFO] 2016-08-16 18:22:51,918 Starting task://016450/P_Filter/subreads.subreads.Gather
[INFO] 2016-08-16 18:23:03,253 task P_Filter.subreads.subreads.Gather successfully completed (2.00 sec (0.03 min)). freed 1 slots, using 1 slots.
[INFO] 2016-08-16 18:23:03,253 Workflow Completion Status 17/74 in (        .. 22%) tasks completed.
[INFO] 2016-08-16 18:23:08,261 Starting task://016450/P_PreAssemblerDagcon/filterLongReadsByLength
[INFO] 2016-08-16 18:23:14,471 task P_Filter.subreads.subreadFastq.Gather successfully completed (5.00 sec (0.08 min)). freed 1 slots, using 1 slots.
[INFO] 2016-08-16 18:23:14,471 Workflow Completion Status 18/74 in (        .. 24%) tasks completed.
[INFO] 2016-08-16 18:23:24,501 task P_PreAssemblerDagcon.filterLongReadsByLength successfully completed (10.00 sec (0.17 min)). freed 1 slots, using 0 slots.
[INFO] 2016-08-16 18:23:24,501 Workflow Completion Status 19/74 in (        .. 25%) tasks completed.
[INFO] 2016-08-16 18:23:29,504 Starting task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection.target.Scatter
[INFO] 2016-08-16 18:23:40,953 task P_PreAssemblerDagcon.hgapAlignForCorrection.target.Scatter successfully completed (3.00 sec (0.05 min)). freed 1 slots, using 0 slots.
[INFO] 2016-08-16 18:23:40,954 Workflow Completion Status 20/74 in (        .. 27%) tasks completed.
[INFO] 2016-08-16 18:23:45,967 Starting task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_005of006
[INFO] 2016-08-16 18:23:45,968 Starting task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_003of006
[INFO] 2016-08-16 18:23:45,968 Starting task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_002of006
[INFO] 2016-08-16 18:23:45,969 Starting task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_006of006
[INFO] 2016-08-16 18:23:45,969 Starting task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_004of006
[INFO] 2016-08-16 18:23:45,969 Starting task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_001of006
[ERROR] 2016-08-16 18:23:45,970 *** Failed task task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_003of006
[ERROR] 2016-08-16 18:23:45,970 *** Failed task task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_005of006
[ERROR] 2016-08-16 18:23:45,971 *** Failed task task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_002of006
[ERROR] 2016-08-16 18:23:45,971 *** Failed task task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_006of006
[ERROR] 2016-08-16 18:23:45,971 *** Failed task task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_004of006
[ERROR] 2016-08-16 18:23:45,972 *** Failed task task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_001of006
[INFO] 2016-08-16 18:23:45,973 Found 6 failed tasks.
[INFO] 2016-08-16 18:23:45,974 task hgapAlignForCorrection_002of006 FAILED 
[INFO] 2016-08-16 18:23:45,974 task hgapAlignForCorrection_003of006 FAILED 
[INFO] 2016-08-16 18:23:45,975 task hgapAlignForCorrection_005of006 FAILED 
[INFO] 2016-08-16 18:23:45,975 task hgapAlignForCorrection_004of006 FAILED 
[INFO] 2016-08-16 18:23:45,976 task hgapAlignForCorrection_006of006 FAILED 
[INFO] 2016-08-16 18:23:45,976 task hgapAlignForCorrection_001of006 FAILED 
[INFO] 2016-08-16 18:23:48,072 Sending Job 016450 failed message 'Exiting smrtpipe last error: SmrtExit task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_002of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_003of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_005of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_004of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_006of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_001of006 Failed' to url http://rgs11.research.partners.org:8080/smrtportal/api/jobs/016450/status
Failed smrtpipe version v1.87.139483 with exit code -1 in 525.62 seconds (8.76 minutes)