Question: Error mapping in RS_Resquensing.1 SMRT portal
0
gravatar for Medhat
6.3 years ago by
Medhat8.8k
Texas
Medhat8.8k wrote:

I am using 18 cell in protocol RS_Resquensing.1 SMRT portal using default parameter.

The process failed raising this error

​[INFO] 2014-09-04 20:27:12,815 [smrtpipe.status refreshTargets 407] task P_Filter.subreads.subreadFastq.Gather successfully completed (1465.00 sec (24.42 min)). freed 1 slots, using 11 slots.
[INFO] 2014-09-04 20:27:12,833 [smrtpipe.status refreshTargets 409] Workflow Completion Status 36/52 in ( ...... 69%) tasks completed.
[ERROR] 2014-09-04 20:48:10,531 [smrtpipe.status refreshTargets 413] *** Failed task task://016452/P_Mapping/align
[INFO] 2014-09-04 20:48:10,562 [smrtpipe.status execute 627] Found 1 failed tasks.
[INFO] 2014-09-04 20:48:10,562 [smrtpipe.status execute 629] task align FAILED
[ERROR] 2014-09-04 20:48:12,710 [SMRTpipe.SmrtPipeMain run 608] SmrtExit task://016452/P_Mapping/align Failed
Traceback (most recent call last):
File "/data/smrtAnalysis/current/redist/python2.7/lib/python2.7/site-packages/SMRTpipe/SmrtPipeMain.py", line 571, in run
self._runTasks(pModules)
File "/data/smrtAnalysis/current/redist/python2.7/lib/python2.7/site-packages/SMRTpipe/SmrtPipeMain.py", line 300, in _runTasks
workflow.execute()​[INFO] 2014-09-04 20:27:12,815 [smrtpipe.status refreshTargets 407] task P_Filter.subreads.subreadFastq.Gather successfully completed (1465.00 sec (24.42 min)). freed 1 slots, using 11 slots.
[INFO] 2014-09-04 20:27:12,833 [smrtpipe.status refreshTargets 409] Workflow Completion Status 36/52 in ( ...... 69%) tasks completed.
[ERROR] 2014-09-04 20:48:10,531 [smrtpipe.status refreshTargets 413] *** Failed task task://016452/P_Mapping/align
[INFO] 2014-09-04 20:48:10,562 [smrtpipe.status execute 627] Found 1 failed tasks.
[INFO] 2014-09-04 20:48:10,562 [smrtpipe.status execute 629] task align FAILED 
[ERROR] 2014-09-0
File "/data/smrtAnalysis/current/redist/python2.7/lib/python2.7/site-packages/SMRTpipe/engine/SmrtPipeWorkflow.py", line 640, in execute
raise SmrtExit(str(e))
SmrtExit: SmrtExit task://016452/P_Mapping/align Failed
[ERROR] 2014-09-04 20:48:12,720 [SMRTpipe.SmrtPipeMain exit 690] SmrtExit task://016452/P_Mapping/align Failed
[INFO] 2014-09-04 20:48:12,720 [SMRTpipe.SmrtPipeMain exit 692] Beginning exit process
[INFO] 2014-09-04 20:48:12,720 [SMRTpipe.SmrtPipeMain shutdown 716] beginning Shutdown Process
[INFO] 2014-09-04 20:48:12,720 [SMRTpipe.SmrtPipeMain _generate_final_report 651] Writing final TOC page with error message : SmrtExit task://016452/P_Mapping/align Failed
[INFO] 2014-09-04 20:48:15,746 [SMRTpipe.SmrtPipeMain shutdown 752] Completed shutdown gracefully
[INFO] 2014-09-04 20:48:15,746 [SMRTpipe.SmrtPipeMain exit 702] Sending message Exiting smrtpipe last error: SmrtExit task://016452/P_Mapping/align Failed
[INFO] 2014-09-04 20:48:15,746 [smrtpipe.status failed 104] Sending Job 016452 failed message 'Exiting smrtpipe last error: SmrtExit task://016452/P_Mapping/align Failed' to url http://150.254.123.63:7070/smrtportal/api/jobs/016452/status
[INFO] 2014-09-04 20:48:16,008 [SMRTpipe.SmrtPipeMain run 641] completed SmrtPipeMain.run with exit code -1
[INFO] 2014-09-04 20:48:16,008 [root main 336] Failed smrtpipe version v1.85.133289 with exit code -1 in 21123.44 seconds (352.06 minutes)

 

 

SMRT portal is setup on my pc  having 12 cpu and 32 G ram

 

Thanks,

ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by Medhat8.8k
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