Comments (1)
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
from rubra.
Related Issues (20)
- Make the pipeline a required argument and remove the --pipeline flag HOT 1
- Modules in the pipeline script's directory can't be imported when it is called via rubra HOT 1
- Add an example pipeline that makes use of the config files
- Putting too many steps out of order results in an error that is not usually seen in Ruffus
- Allow module loading for non-distributed jobs HOT 1
- Support SLURM job scheduler HOT 2
- Allow config file to be in different directory to pipeline file
- save a separate shell script for each submitted job
- Generate other image format types for flowchart
- Use shlex.split to parse srun command line
- Make rubra more robust in the face of job errors
- handling of full paths in command line
- example doesn't run out of the box HOT 1
- Trouble install directly from pip HOT 1
- Make Rubra an installable package in the normal Python way. HOT 1
- Investigate the use of DRMAA to submit jobs to clusters. HOT 2
- Make the installed rubra package executable as a script from the user's path HOT 2
- Add touchfiles as an option alongside print, run, flowchart HOT 2
- The default of rebuild appears to actually be fromstart (which I would expect) ? But docs say it is fromend. HOT 1
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from rubra.