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msk-access / access_qc_generation

Generation Quality Controls Files for MSK-ACCESS
https://cmo-ci.gitbook.io/access-quality-control-v2/
Apache License 2.0
1 stars 1 forks source link

CWL_UNSUPPORTED_REQUIREMENT_EXIT_CODE #9

Open ionox0 opened 3 years ago

ionox0 commented 3 years ago 
...
        self.add_file_or_directory_volume(runtime, vol, host_outdir_tgt)
      File "/home/accessbot/miniconda3/envs/toil_test/lib/python3.7/site-packages/cwltool/singularity.py", line 310, in add_file_or_directory_volume
        shutil.copytree(volume.resolved, host_outdir_tgt)
      File "/home/accessbot/miniconda3/envs/toil_test/lib/python3.7/shutil.py", line 318, in copytree
        names = os.listdir(src)
    FileNotFoundError: [Errno 2] No such file or directory: '_:4694b3bc-a86a-4be4-8d99-b6876552c8a8'

    The above exception was the direct cause of the following exception:

    Traceback (most recent call last):
      File "/home/accessbot/miniconda3/envs/toil_test/lib/python3.7/site-packages/toil/worker.py", line 400, in workerScript
        job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer)
      File "/home/accessbot/miniconda3/envs/toil_test/lib/python3.7/site-packages/toil/job.py", line 2382, in _runner
        returnValues = self._run(jobGraph=None, fileStore=fileStore)
      File "/home/accessbot/miniconda3/envs/toil_test/lib/python3.7/site-packages/toil/job.py", line 2303, in _run
        return self.run(fileStore)
      File "/home/accessbot/miniconda3/envs/toil_test/lib/python3.7/site-packages/toil/cwl/cwltoil.py", line 1921, in run
        logger=cwllogger,
      File "/home/accessbot/miniconda3/envs/toil_test/lib/python3.7/site-packages/cwltool/executors.py", line 149, in execute
        self.run_jobs(process, job_order_object, logger, runtime_context)
      File "/home/accessbot/miniconda3/envs/toil_test/lib/python3.7/site-packages/toil/cwl/cwltoil.py", line 848, in run_jobs
        return super().run_jobs(process, job_order_object, logger, runtime_context)
      File "/home/accessbot/miniconda3/envs/toil_test/lib/python3.7/site-packages/cwltool/executors.py", line 267, in run_jobs
        raise WorkflowException(str(err)) from err
    cwltool.errors.WorkflowException: [Errno 2] No such file or directory: '_:4694b3bc-a86a-4be4-8d99-b6876552c8a8'
    [2021-07-01T15:49:09-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host jx04
<=========
[2021-07-01T15:54:22-0400] [MainThread] [E] [root] Your workflow uses a CWL requirement that Toil does not support!