I am trying to run the modification and motif analysis in the SMRTportal. It completes the resequencing component ok but then it fails and i’m not sure why. I get the following in the log (included from the error message onwards)
…
[INFO] 2018-02-27 20:47:29,752 [smrtpipe.status refreshTargets 419] Starting task://016443/P_Mapping/gff2Bed
[ERROR] 2018-02-28 08:47:49,684 [smrtpipe.status refreshTargets 413] *** Failed task task://016443/P_ModificationDetection/computeModifications_001of001
[INFO] 2018-02-28 08:47:53,048 [smrtpipe.status execute 627] Found 1 failed tasks.
[INFO] 2018-02-28 08:47:53,048 [smrtpipe.status execute 629] task computeModifications_001of001 FAILED
[ERROR] 2018-02-28 08:47:56,551 [SMRTpipe.SmrtPipeMain run 608] SmrtExit task://016443/P_ModificationDetection/computeModifications_001of001 Failed
Traceback (most recent call last):
File “/mnt/gvl/apps/smrtanalysis/install/smrtanalysis_2.3.0.140936/redist/python2.7/lib/python2.7/site-packages/SMRTpipe/SmrtPipeMain.py”, line 571, in run
self._runTasks(pModules)
File “/mnt/gvl/apps/smrtanalysis/install/smrtanalysis_2.3.0.140936/redist/python2.7/lib/python2.7/site-packages/SMRTpipe/SmrtPipeMain.py”, line 300, in _runTasks
workflow.execute()
File “/mnt/gvl/apps/smrtanalysis/install/smrtanalysis_2.3.0.140936/redist/python2.7/lib/python2.7/site-packages/SMRTpipe/engine/SmrtPipeWorkflow.py”, line 640, in execute
raise SmrtExit(str(e))
SmrtExit: SmrtExit task://016443/P_ModificationDetection/computeModifications_001of001 Failed
[ERROR] 2018-02-28 08:47:56,562 [SMRTpipe.SmrtPipeMain exit 690] SmrtExit task://016443/P_ModificationDetection/computeModifications_001of001 Failed
[INFO] 2018-02-28 08:47:56,562 [SMRTpipe.SmrtPipeMain exit 692] Beginning exit process
[INFO] 2018-02-28 08:47:56,562 [SMRTpipe.SmrtPipeMain shutdown 716] beginning Shutdown Process
[INFO] 2018-02-28 08:47:56,562 [SMRTpipe.SmrtPipeMain _generate_final_report 651] Writing final TOC page with error message : SmrtExit task://016443/P_ModificationDetection/computeModifications_001of001 Failed
[INFO] 2018-02-28 08:47:57,217 [SMRTpipe.SmrtPipeMain shutdown 752] Completed shutdown gracefully
[INFO] 2018-02-28 08:47:57,218 [SMRTpipe.SmrtPipeMain exit 702] Sending message Exiting smrtpipe last error: SmrtExit task://016443/P_ModificationDetection/computeModifications_001of001 Failed
[INFO] 2018-02-28 08:47:57,218 [smrtpipe.status failed 104] Sending Job 016443 failed message ‘Exiting smrtpipe last error: SmrtExit task://016443/P_ModificationDetection/computeModifications_001of001 Failed’ to url http://127.0.0.1:9080/smrtportal/api/jobs/016443/status
[INFO] 2018-02-28 08:47:57,335 [SMRTpipe.SmrtPipeMain run 641] completed SmrtPipeMain.run with exit code -1
[INFO] 2018-02-28 08:47:57,335 [root main 335] Failed smrtpipe version v1.87.139483 with exit code -1 in 74046.11 seconds (1234.10 minutes)
Do you know what’s causing it to fail and how i can fix it?
Many thanks.