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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
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toil mutex filenotfound error #8

Open ionox0 opened 3 years ago

ionox0 commented 3 years ago

Just putting this here to keep track, it appears to be sporadic and is fixed with a retry

<=========
[2021-07-01T14:58:39-0400] [Thread-261] [D] [toil.batchSystems.singleMachine] Launched job 240 as child 20646
Traceback (most recent call last):
  File "/home/accessbot/miniconda3/envs/toil_test/bin/_toil_worker", line 8, in <module>
    sys.exit(main())
  File "/home/accessbot/miniconda3/envs/toil_test/lib/python3.7/site-packages/toil/worker.py", line 704, in main
    with in_contexts(options.context):
  File "/home/accessbot/miniconda3/envs/toil_test/lib/python3.7/contextlib.py", line 112, in __enter__
    return next(self.gen)
  File "/home/accessbot/miniconda3/envs/toil_test/lib/python3.7/site-packages/toil/worker.py", line 678, in in_contexts
    with manager:
  File "/home/accessbot/miniconda3/envs/toil_test/lib/python3.7/site-packages/toil/batchSystems/abstractBatchSystem.py", line 494, in __enter__
    self.arena.enter()
  File "/home/accessbot/miniconda3/envs/toil_test/lib/python3.7/site-packages/toil/lib/threading.py", line 448, in enter
    fcntl.lockf(self.lockfileFD, fcntl.LOCK_EX) # type: ignore
  File "/home/accessbot/miniconda3/envs/toil_test/lib/python3.7/contextlib.py", line 119, in __exit__
    next(self.gen)
  File "/home/accessbot/miniconda3/envs/toil_test/lib/python3.7/site-packages/toil/lib/threading.py", line 366, in global_mutex
    os.unlink(lock_filename)
FileNotFoundError: [Errno 2] No such file or directory: '/juno/work/access/testing/users/johnsoni/access_qc/5500_HE/work/toil-mutex-cf0426ab-aa3d-4829-a54f-c264832f82aa-cleanup-arena-lock'