[INFO] 2016-08-10 18:04:30,491 Successfully found 3 files in xml:/PHShome/ry077/bin/smrtanalysis/userdata/jobs/016/016445/input.xml
[INFO] 2016-08-10 18:04:31,541 smrtpipe.py running on rgs11.research.partners.org
[INFO] 2016-08-10 18:04:31,541 SMRT Analysis 2.3.0 / SMRTpipe 1.87.139483
[INFO] 2016-08-10 18:04:35,602 Process id 54604
[INFO] 2016-08-10 18:04:42,605 Starting task://016445/P_Fetch/toFofn
[INFO] 2016-08-10 18:04:42,618 task P_Fetch.toFofn successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 0 slots.
[INFO] 2016-08-10 18:04:42,618 Workflow Completion Status 1/74 in (            1%) tasks completed.
[INFO] 2016-08-10 18:04:47,626 Starting task://016445/P_Fetch/adapterRpt
[INFO] 2016-08-10 18:04:47,627 Starting task://016445/P_Mapping/align.plsFofn.Scatter
[INFO] 2016-08-10 18:04:47,627 Starting task://016445/P_Fetch/overviewRpt
[INFO] 2016-08-10 18:04:47,647 task P_Mapping.align.plsFofn.Scatter successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 2 slots.
[INFO] 2016-08-10 18:04:47,647 Workflow Completion Status 2/74 in (            2%) tasks completed.
[INFO] 2016-08-10 18:04:52,657 Starting task://016445/P_Filter/filter_002of003
[INFO] 2016-08-10 18:04:52,657 Starting task://016445/P_Filter/filter_003of003
[INFO] 2016-08-10 18:04:52,657 Starting task://016445/P_Filter/filter_001of003
[INFO] 2016-08-10 23:23:55,489 task P_Fetch.overviewRpt successfully completed (11.00 sec (0.18 min)). freed 1 slots, using 7 slots.
[INFO] 2016-08-10 23:23:55,492 Workflow Completion Status 3/74 in (            4%) tasks completed.
[INFO] 2016-08-10 23:24:23,238 task P_Fetch.adapterRpt successfully completed (41.00 sec (0.68 min)). freed 1 slots, using 6 slots.
[INFO] 2016-08-10 23:24:23,238 Workflow Completion Status 4/74 in (            5%) tasks completed.
[INFO] 2016-08-10 23:24:28,280 task P_Filter.filter_003of003 successfully completed (45.00 sec (0.75 min)). freed 2 slots, using 4 slots.
[INFO] 2016-08-10 23:24:28,280 Workflow Completion Status 5/74 in (            6%) tasks completed.
[INFO] 2016-08-10 23:24:28,309 task P_Filter.filter_001of003 successfully completed (45.00 sec (0.75 min)). freed 2 slots, using 2 slots.
[INFO] 2016-08-10 23:24:28,309 Workflow Completion Status 6/74 in (            8%) tasks completed.
[INFO] 2016-08-10 23:24:33,314 Starting task://016445/P_Filter/subreads_003of003
[INFO] 2016-08-10 23:24:33,315 Starting task://016445/P_Filter/subreads_001of003
[INFO] 2016-08-10 23:24:38,354 task P_Filter.filter_002of003 successfully completed (57.00 sec (0.95 min)). freed 2 slots, using 2 slots.
[INFO] 2016-08-10 23:24:38,354 Workflow Completion Status 7/74 in (            9%) tasks completed.
[INFO] 2016-08-10 23:24:43,363 Starting task://016445/P_Filter/subreads_002of003
[INFO] 2016-08-10 23:24:43,363 Starting task://016445/P_Filter/filter.summary.Gather
[INFO] 2016-08-10 23:24:43,364 Starting task://016445/P_Filter/filter.rgnFofn.Gather
[INFO] 2016-08-10 23:24:43,382 task P_Filter.filter.rgnFofn.Gather successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 4 slots.
[INFO] 2016-08-10 23:24:43,383 Workflow Completion Status 8/74 in (         . 10%) tasks completed.
[INFO] 2016-08-10 23:24:48,390 Starting task://016445/P_Filter/subreadSummary
[INFO] 2016-08-10 23:25:11,308 task P_Filter.filter.summary.Gather successfully completed (1.00 sec (0.02 min)). freed 1 slots, using 4 slots.
[INFO] 2016-08-10 23:25:11,308 Workflow Completion Status 9/74 in (         . 12%) tasks completed.
[INFO] 2016-08-10 23:25:16,317 Starting task://016445/P_FilterReports/statsRpt
[INFO] 2016-08-10 23:25:16,318 Starting task://016445/P_FilterReports/loadingRpt
[INFO] 2016-08-10 23:25:56,372 task P_Filter.subreads_003of003 successfully completed (52.00 sec (0.87 min)). freed 1 slots, using 5 slots.
[INFO] 2016-08-10 23:25:56,372 Workflow Completion Status 10/74 in (         . 13%) tasks completed.
[INFO] 2016-08-10 23:26:01,395 task P_Filter.subreads_001of003 successfully completed (58.00 sec (0.97 min)). freed 1 slots, using 4 slots.
[INFO] 2016-08-10 23:26:01,395 Workflow Completion Status 11/74 in (         . 14%) tasks completed.
[INFO] 2016-08-10 23:26:02,733 task P_FilterReports.loadingRpt successfully completed (8.00 sec (0.13 min)). freed 1 slots, using 3 slots.
[INFO] 2016-08-10 23:26:02,733 Workflow Completion Status 12/74 in (         . 16%) tasks completed.
[INFO] 2016-08-10 23:26:02,751 task P_Filter.subreads_002of003 successfully completed (60.00 sec (1.00 min)). freed 1 slots, using 2 slots.
[INFO] 2016-08-10 23:26:02,752 Workflow Completion Status 13/74 in (         . 17%) tasks completed.
[INFO] 2016-08-10 23:26:07,759 Starting task://016445/P_Filter/subreads.subreads.Gather
[INFO] 2016-08-10 23:26:07,759 Starting task://016445/P_Filter/subreads.subreadFastq.Gather
[INFO] 2016-08-10 23:26:15,372 task P_FilterReports.statsRpt successfully completed (15.00 sec (0.25 min)). freed 1 slots, using 3 slots.
[INFO] 2016-08-10 23:26:15,372 Workflow Completion Status 14/74 in (         . 18%) tasks completed.
[INFO] 2016-08-10 23:26:21,719 task P_Filter.subreadSummary successfully completed (31.00 sec (0.52 min)). freed 1 slots, using 2 slots.
[INFO] 2016-08-10 23:26:21,720 Workflow Completion Status 15/74 in (        .. 20%) tasks completed.
[INFO] 2016-08-10 23:26:26,726 Starting task://016445/P_FilterReports/subreadRpt
[INFO] 2016-08-10 23:27:59,650 task P_Filter.subreads.subreads.Gather successfully completed (2.00 sec (0.03 min)). freed 1 slots, using 2 slots.
[INFO] 2016-08-10 23:27:59,651 Workflow Completion Status 16/74 in (        .. 21%) tasks completed.
[INFO] 2016-08-10 23:28:00,907 task P_FilterReports.subreadRpt successfully completed (5.00 sec (0.08 min)). freed 1 slots, using 1 slots.
[INFO] 2016-08-10 23:28:00,908 Workflow Completion Status 17/74 in (        .. 22%) tasks completed.
[INFO] 2016-08-10 23:28:02,114 task P_Filter.subreads.subreadFastq.Gather successfully completed (6.00 sec (0.10 min)). freed 1 slots, using 0 slots.
[INFO] 2016-08-10 23:28:02,114 Workflow Completion Status 18/74 in (        .. 24%) tasks completed.
[INFO] 2016-08-10 23:28:07,121 Starting task://016445/P_PreAssemblerDagcon/filterLongReadsByLength
[INFO] 2016-08-10 23:28:53,640 task P_PreAssemblerDagcon.filterLongReadsByLength successfully completed (10.00 sec (0.17 min)). freed 1 slots, using 0 slots.
[INFO] 2016-08-10 23:28:53,641 Workflow Completion Status 19/74 in (        .. 25%) tasks completed.
[INFO] 2016-08-10 23:28:58,648 Starting task://016445/P_PreAssemblerDagcon/hgapAlignForCorrection.target.Scatter
[INFO] 2016-08-10 23:29:40,134 task P_PreAssemblerDagcon.hgapAlignForCorrection.target.Scatter successfully completed (13.00 sec (0.22 min)). freed 1 slots, using 0 slots.
[INFO] 2016-08-10 23:29:40,134 Workflow Completion Status 20/74 in (        .. 27%) tasks completed.
[INFO] 2016-08-10 23:29:45,144 Starting task://016445/P_PreAssemblerDagcon/hgapAlignForCorrection_005of006
[INFO] 2016-08-10 23:29:45,145 Starting task://016445/P_PreAssemblerDagcon/hgapAlignForCorrection_001of006
[INFO] 2016-08-10 23:29:45,145 Starting task://016445/P_PreAssemblerDagcon/hgapAlignForCorrection_006of006
[INFO] 2016-08-10 23:29:45,145 Starting task://016445/P_PreAssemblerDagcon/hgapAlignForCorrection_002of006
[INFO] 2016-08-10 23:29:45,146 Starting task://016445/P_PreAssemblerDagcon/hgapAlignForCorrection_003of006
[INFO] 2016-08-10 23:29:45,146 Starting task://016445/P_PreAssemblerDagcon/hgapAlignForCorrection_004of006
[ERROR] 2016-08-10 23:29:45,147 *** Failed task task://016445/P_PreAssemblerDagcon/hgapAlignForCorrection_001of006
[ERROR] 2016-08-10 23:29:45,147 *** Failed task task://016445/P_PreAssemblerDagcon/hgapAlignForCorrection_005of006
[ERROR] 2016-08-10 23:29:45,148 *** Failed task task://016445/P_PreAssemblerDagcon/hgapAlignForCorrection_006of006
[ERROR] 2016-08-10 23:29:45,148 *** Failed task task://016445/P_PreAssemblerDagcon/hgapAlignForCorrection_003of006
[ERROR] 2016-08-10 23:29:45,149 *** Failed task task://016445/P_PreAssemblerDagcon/hgapAlignForCorrection_002of006
[ERROR] 2016-08-10 23:29:45,149 *** Failed task task://016445/P_PreAssemblerDagcon/hgapAlignForCorrection_004of006
[INFO] 2016-08-10 23:29:45,151 Found 6 failed tasks.
[INFO] 2016-08-10 23:29:45,151 task hgapAlignForCorrection_003of006 FAILED 
[INFO] 2016-08-10 23:29:45,152 task hgapAlignForCorrection_004of006 FAILED 
[INFO] 2016-08-10 23:29:45,152 task hgapAlignForCorrection_001of006 FAILED 
[INFO] 2016-08-10 23:29:45,153 task hgapAlignForCorrection_002of006 FAILED 
[INFO] 2016-08-10 23:29:45,154 task hgapAlignForCorrection_006of006 FAILED 
[INFO] 2016-08-10 23:29:45,154 task hgapAlignForCorrection_005of006 FAILED 
[INFO] 2016-08-10 23:29:47,494 Sending Job 016445 failed message 'Exiting smrtpipe last error: SmrtExit task://016445/P_PreAssemblerDagcon/hgapAlignForCorrection_003of006 Failed task://016445/P_PreAssemblerDagcon/hgapAlignForCorrection_004of006 Failed task://016445/P_PreAssemblerDagcon/hgapAlignForCorrection_001of006 Failed task://016445/P_PreAssemblerDagcon/hgapAlignForCorrection_002of006 Failed task://016445/P_PreAssemblerDagcon/hgapAlignForCorrection_006of006 Failed task://016445/P_PreAssemblerDagcon/hgapAlignForCorrection_005of006 Failed' to url http://rgs11.research.partners.org:8080/smrtportal/api/jobs/016445/status
Failed smrtpipe version v1.87.139483 with exit code -1 in 19517.02 seconds (325.28 minutes)