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katholt
qsub command failed with exit status: 172
Hello, I am running the pipeline and I am getting this error, could you help me? Thanks!
Starting pipeline...
155 jobs to be executed in total
Traceback (most recent call last):
File "/usr/local/bin/rubra", line 11, in
Exceptions running jobs for
'def RedDog.makeDir(...):'
Original exception:
Exception #1
exceptions.Exception(qsub command failed with exit status: 172):
for RedDog.makeDir.Job = [False -> dir.makeDir.Success]
Traceback (most recent call last):
File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 517, in run_pooled_job_without_exceptions
return_value = job_wrapper(param, user_defined_work_func, register_cleanup, touch_files_only)
File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 447, in job_wrapper_io_files
ret_val = user_defined_work_func(*param)
File "RedDog.py", line 955, in makeDir
runStageCheck('makeDir', flagFile, outPrefix, full_sequence_list_string)
File "build/bdist.linux-x86_64/egg/rubra/utils.py", line 128, in runStageCheck
status = runStage(stage, *args)
File "build/bdist.linux-x86_64/egg/rubra/utils.py", line 144, in runStage
exitStatus = distributedCommand(stage, commandStr, pipeline_options)
File "build/bdist.linux-x86_64/egg/rubra/utils.py", line 122, in distributedCommand
return script.runJobAndWait(stage, logDir, verbosity)
File "build/bdist.linux-x86_64/egg/rubra/cluster_job.py", line 65, in runJobAndWait
jobID = self.launch()
File "build/bdist.linux-x86_64/egg/rubra/cluster_job.py", line 138, in launch
str(returnCode)))
Exception: qsub command failed with exit status: 172
Are you running on a torque/qsub system or a SLURM system (or indeed another OS)?
I am running on a torque/qsub system. Which system does RedDog use?
El martes, 18 de diciembre de 2018, d-j-e [email protected] escribió:
Are you running on a torque/qsub system or a SLURM system (or indeed another OS)?
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/katholt/RedDog/issues/60#issuecomment-448387873, or mute the thread https://github.com/notifications/unsubscribe-auth/Ar2QjJETL5FUOGjmFHIrh_i8PaSf-Z71ks5u6WZLgaJpZM4ZY2Le .
-- Lic. Verónica E. Álvarez Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos IMPAM (UBA/CONICET) Facultad de Medicina Universidad de Buenos Aires +54 11 5950-9500 x 2182
RedDog is actually 'system neutral'; it is Rubra that controls the job submissions to the relevant queue. Though reddog was originally written on a 'qsub' system so it should have no problems...
I cannot find a description of qsub exit status 172 - it is not a 'reserved' code so you may have to seek the help of a local system administrator to work out what the error means. This first step creates all the output directories required for the run, so it might be a permissions error of some kind, but that is only a guess. You could also try raising the issue on the rubra github page.
Ok, thank you for your suggestions.
Regards.
El mié., 19 dic. 2018 a las 19:23, d-j-e ([email protected]) escribió:
RedDog is actually 'system neutral'; it is Rubra that controls the job submissions to the relevant queue. Though reddog was originally written on a 'qsub' system so it should have no problems...
I cannot find a description of qsub exit status 172 - it is not a 'reserved' code so you may have to seek the help of a local system administrator to work out what the error means. This first step creates all the output directories required for the run, so it might be a permissions error of some kind, but that is only a guess. You could also try raising the issue on the rubra github page.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/katholt/RedDog/issues/60#issuecomment-448765267, or mute the thread https://github.com/notifications/unsubscribe-auth/Ar2QjBTylwW4XT2vnHoaZV88S24iR9cXks5u6rxfgaJpZM4ZY2Le .
-- Lic. Verónica E. Álvarez Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos IMPAM (UBA/CONICET) Facultad de Medicina Universidad de Buenos Aires +54 11 5950-9500 x 2182