Task_Cluster_Job Script::: Ruffus and Rubra Infrstructure

[Olabode Ajayi]

Good day all,

I am currently adapting and reproducing a variants calling python scripts, and why trying to understand how the script works. I started getting errors regarding rubra and ruffus PBS/SGE, a cluster_job.py. Our SANBI cluster uses SGE torque and I don't know how I will go about editing the Rubra Cluster_job.py script. Maybe, there is better way to modify the rubra cluster_job.py script for SGE configuration.

 The following are the errors I am getting when I run the scripts and I set the config_field for job distribution on cluster to be True.

Symlinked files that will be used:

/cip0/research/ajayi/workflows/example_data/output_wgs/fastq_symlinks/NA12878wgs_20FUKAAXX_L6_1.fastq.gz

/cip0/research/ajayi/workflows/example_data/output_wgs/fastq_symlinks/NA12878wgs_20FUKAAXX_L6_2.fastq.gz

Output dir is /cip0/research/ajayi/workflows/example_data/output_wgs

Log dir is log_example_wgs

stage = fastqc, jobID = Your job 7493843 ("tmpXL92BT") has been submitted

stage = fastqc, jobID = Your job 7493842 ("tmpihkNU0") has been submitted

Traceback (most recent call last):

  File "/usr/local/bin/rubra", line 9, in <module>

    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 pipeTest.fastqc(...):'

    

    Original exceptions:

    

    Exception #1

    exceptions.Exception(qstat -f Your job 7493842 ("tmpihkNU0") has been submitted

     returned non-zero exit status 5 times,                             panicking):

    for pipeTest.fastqc.Job = [NA12878wgs_20FUKAAXX_L6_1.fastq.gz -> [NA12878wgs_20FUKAAXX_L6_1_fastqc, NA12878wgs_20FUKAAXX_L6_1.fastqc.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 "pipeTest.py", line 121, in fastqc

        runStageCheck('fastqc', flagFile, fastqc_dir, sequence)

      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 72, in runJobAndWait

        return self.waitForJobCompletion(jobID)

      File "build/bdist.linux-x86_64/egg/rubra/cluster_job.py", line 56, in waitForJobCompletion

        isFinished, exitCode = self.isJobCompleted(jobID)

      File "build/bdist.linux-x86_64/egg/rubra/cluster_job.py", line 32, in isJobCompleted

        panicking" % (jobID, count))

    Exception: qstat -f Your job 7493842 ("tmpihkNU0") has been submitted

     returned non-zero exit status 5 times,                             panicking

    

    

    Exception #2

    exceptions.Exception(qstat -f Your job 7493843 ("tmpXL92BT") has been submitted

     returned non-zero exit status 5 times,                             panicking):

    for pipeTest.fastqc.Job = [NA12878wgs_20FUKAAXX_L6_2.fastq.gz -> [NA12878wgs_20FUKAAXX_L6_2_fastqc, NA12878wgs_20FUKAAXX_L6_2.fastqc.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 "pipeTest.py", line 121, in fastqc

        runStageCheck('fastqc', flagFile, fastqc_dir, sequence)

      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 72, in runJobAndWait

        return self.waitForJobCompletion(jobID)

      File "build/bdist.linux-x86_64/egg/rubra/cluster_job.py", line 56, in waitForJobCompletion

        isFinished, exitCode = self.isJobCompleted(jobID)

      File "build/bdist.linux-x86_64/egg/rubra/cluster_job.py", line 32, in isJobCompleted

        panicking" % (jobID, count))

    Exception: qstat -f Your job 7493843 ("tmpXL92BT") has been submitted

     returned non-zero exit status 5 times,                             panicking

Perhaps, Is there something I was doing wrong become as its stand now. I am very retard in debugging.

Here is a link to Rubra cluster.py script: https://github.com/bjpop/rubra/blob/master/rubra/cluster_job.py

Here is also setting for my pipeline_stage_config.py:

stageDefaults = {

    'distributed': True,

    'queue': None,

    'walltime': "01:00:00",

    'memInGB': 8,

     'modules': [

        "bwa/bwa-0.7.8",

        "samtools/samtools-0.1.19",

        "python-gcc/2.7.6",

        "picard-tools/picard-tools-1.115"

     ]

}

# stages should hold the details of each stage which can be called by runStageCheck.

# This section is required for every Rubra pipeline.

# Calling a stage in this way carries out checkpointing and, if desired, batch job

# submission. 

# Each stage must contain a 'command' definition. See stageDefaults above for other 

# allowable options.

stages = {

    "fastqc": {

        "command": "fastqc --quiet -o %outdir %seq",

        'modules': [ "fastqc/0.11.4" ]

    },

    "bwaMemPE": {

        "command": "bwa mem -t 8 %meta %ref %seq1 %seq2 > %out",

        'walltime': "3:00:00",

        'queue': 'long.q',

I would appreciate your input.

Thank you,

Ajayi

[Leo Goodstadt 顧維斌]

Hi Ajayi,

It looks like your fastqc command is not working. Have you tried running the command manually to see if it works? I am afraid I am not familiar enough with rubra to say much more. 

This is Bernie (Pope)'s baby, I think?

Leo

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[Bernard James Pope]

Hi Ajayi,

Thanks for responding Leo.

I'm not sure what is the cause of the problem. However, it could an incompatibility with SGE, which I've never used.

Having said that, we are not using rubra any more, because newer versions of ruffus have included many great features which make rubra more-or-less redundant.

If you want to see what an example of our ruffus pipelines look like these days, here is one for variant calling:

https://github.com/bjpop/complexo_pipeline

Note: this is from my own work, built on top of ruffus. You are welcome to use it if it suits your purposes. However, I probably don't have a lot of resources for trouble-shooting.

Cheers,
Bernie