SMRT analysis modification and motif analysis

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.

Hi Donna - I’m afraid the problem here isn’t immediately obvious to me. The first step of the pipeline at least looks as if it does something (and takes 12 hours to do so), but the failure message isn’t very informative.

I’ll need to dig a bit further into this, and I’ve sent you a PM so that we can start to work it out.

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