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Problems with installation of Quast 5.0.2 on macOS-10.15.7-x86_64-i386-64bit

Open AlWa1 opened this issue 3 years ago • 0 comments

Hi everybody, I just installed the most recent version of Quast, tried to run the test set and got following issue. Anybody that can help or ran into similar issues?

Bests, Alan

(base) alanwanke@slpc459 quast-5.0.2 % ./setup.py test
/Users/alanwanke/opt/anaconda3/lib/python3.9/site-packages/quast-5.0.2-py3.9.egg/EGG-INFO/scripts/quast.py --test

Version: 5.0.2

System information:
  OS: macOS-10.15.7-x86_64-i386-64bit (macosx)
  Python version: 3.9.7
  CPUs number: 16

Started: 2022-03-09 19:46:16

Logging to /Users/alanwanke/quast-5.0.2/quast_test_output/quast.log
NOTICE: Output directory already exists and looks like a QUAST output dir. Existing results can be reused (e.g. previously generated alignments)!
NOTICE: Maximum number of threads is set to 4 (use --threads option to set it manually)

CWD: /Users/alanwanke/quast-5.0.2
Main parameters: 
  MODE: default, threads: 4, minimum contig length: 500, minimum alignment length: 65, \
  ambiguity: one, threshold for extensive misassembly size: 1000

Reference:
  /Users/alanwanke/quast-5.0.2/test_data/reference.fasta.gz ==> reference

Contigs:
  Pre-processing...

module '__main__' has no attribute '__spec__'
Traceback (most recent call last):
  File "/Users/alanwanke/opt/anaconda3/lib/python3.9/site-packages/quast-5.0.2-py3.9.egg/EGG-INFO/scripts/quast.py", line 307, in <module>
    return_code = main(sys.argv[1:])
  File "/Users/alanwanke/opt/anaconda3/lib/python3.9/site-packages/quast-5.0.2-py3.9.egg/EGG-INFO/scripts/quast.py", line 107, in main
    contigs_fpaths, old_contigs_fpaths = qutils.correct_contigs(contigs_fpaths, corrected_dirpath, labels, reporting)
  File "/Users/alanwanke/opt/anaconda3/lib/python3.9/site-packages/quast-5.0.2-py3.9.egg/quast_libs/qutils.py", line 180, in correct_contigs
    old_fpaths, corr_fpaths, broken_scaffold_fpaths, logs, is_fatal_error = run_parallel(parallel_correct_contigs, parallel_run_args, n_jobs)
  File "/Users/alanwanke/opt/anaconda3/lib/python3.9/site-packages/quast-5.0.2-py3.9.egg/quast_libs/qutils.py", line 1065, in run_parallel
    results_tuples = Parallel(**parallel_args)(delayed(_fn)(*args) for args in fn_args)
  File "/Users/alanwanke/opt/anaconda3/lib/python3.9/site-packages/joblib/parallel.py", line 968, in __call__
    n_jobs = self._initialize_backend()
  File "/Users/alanwanke/opt/anaconda3/lib/python3.9/site-packages/joblib/parallel.py", line 735, in _initialize_backend
    n_jobs = self._backend.configure(n_jobs=self.n_jobs, parallel=self,
  File "/Users/alanwanke/opt/anaconda3/lib/python3.9/site-packages/joblib/_parallel_backends.py", line 470, in configure
    self._pool = MemmappingPool(n_jobs, **memmappingpool_args)
  File "/Users/alanwanke/opt/anaconda3/lib/python3.9/site-packages/joblib/pool.py", line 323, in __init__
    super(MemmappingPool, self).__init__(**poolargs)
  File "/Users/alanwanke/opt/anaconda3/lib/python3.9/site-packages/joblib/pool.py", line 205, in __init__
    super(PicklingPool, self).__init__(**poolargs)
  File "/Users/alanwanke/opt/anaconda3/lib/python3.9/multiprocessing/pool.py", line 212, in __init__
    self._repopulate_pool()
  File "/Users/alanwanke/opt/anaconda3/lib/python3.9/multiprocessing/pool.py", line 303, in _repopulate_pool
    return self._repopulate_pool_static(self._ctx, self.Process,
  File "/Users/alanwanke/opt/anaconda3/lib/python3.9/multiprocessing/pool.py", line 326, in _repopulate_pool_static
    w.start()
  File "/Users/alanwanke/opt/anaconda3/lib/python3.9/multiprocessing/process.py", line 121, in start
    self._popen = self._Popen(self)
  File "/Users/alanwanke/opt/anaconda3/lib/python3.9/multiprocessing/context.py", line 284, in _Popen
    return Popen(process_obj)
  File "/Users/alanwanke/opt/anaconda3/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 32, in __init__
    super().__init__(process_obj)
  File "/Users/alanwanke/opt/anaconda3/lib/python3.9/multiprocessing/popen_fork.py", line 19, in __init__
    self._launch(process_obj)
  File "/Users/alanwanke/opt/anaconda3/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 42, in _launch
    prep_data = spawn.get_preparation_data(process_obj._name)
  File "/Users/alanwanke/opt/anaconda3/lib/python3.9/multiprocessing/spawn.py", line 183, in get_preparation_data
    main_mod_name = getattr(main_module.__spec__, "name", None)
AttributeError: module '__main__' has no attribute '__spec__'
ERROR! exception caught!

AlWa1 avatar Mar 09 '22 19:03 AlWa1