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qsub command failed with exit status: 172 #60

Open vealvarez opened 5 years ago

vealvarez commented 5 years ago

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 load_entry_point('Rubra==0.1.5', 'console_scripts', 'rubra')() File "build/bdist.linux-x86_64/egg/rubra/rubra.py", line 66, in main File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 2680, in pipeline_run ruffus.ruffus_exceptions.RethrownJobError:

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
d-j-e commented 5 years ago

Are you running on a torque/qsub system or a SLURM system (or indeed another OS)?

vealvarez commented 5 years ago

I am running on a torque/qsub system. Which system does RedDog use?

El martes, 18 de diciembre de 2018, d-j-e notifications@github.com 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

d-j-e commented 5 years ago

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.

vealvarez commented 5 years ago

Ok, thank you for your suggestions.

Regards.

El mié., 19 dic. 2018 a las 19:23, d-j-e (notifications@github.com) 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