Rubra RedDog error

[vealvarez]

Hello, I am running RedDog and I am getting the error that is detailed below. I reported this problem in RedDog GitHub and they suggested that it could be a problem with Rubra and server permissions. I am running the pipeline on a torque/qsub system. Could you help me? Thanks in advance!

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

[vealvarez]

Hello again, I have ran RedDog using root user and now the error is the following

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: 1):
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: 1