[scipion-users] xmipp - validate overfilling protocol isue

[Dmitry S. <Sem...@gm...>]

Dear colleagues,

Issue while using xmipp - validate overfilling protocol




_ERROR 1: Errors on command line parameters
Unrecognized parameter: --thr

[1;31mFile: core/argsparser.cpp line: 1005[0m
For more info use --help
[1;31mXMIPP_ERROR 1: Errors on command line parameters[0m
[1;31m[1;31mUnrecognized parameter: --thr
[0m[0m
[1;31mFile: core/argsparser.cpp line: 1005[0m
For more info use --help
Traceback (most recent call last):
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 201, in run
    self._run()
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 252, in _run
    resultFiles = self._runFunc()
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _runFunc
    return self._func(*self._args)
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/xmipp3/protocols/protocol_validate_overfitting.py", line 362, in reconstructionStep
    self.runJob('xmipp_reconstruct_fourier_accel', params)
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1388, in runJob
    self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob
    process.runJob(log, programName, params,
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob
    return runCommand(command, env, cwd)
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand
    check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
  File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command ' mpirun -np 8  `which xmipp_mpi_reconstruct_fourier_accel`   -i Runs/008120_XmippProtValidateOverfitting/extra/Nfraction_alignment00_00_00.xmd  -o Runs/008120_XmippProtValidateOverfitting/extra/Nfraction00_00_00.vol --sym c2 --max_resolution 0.500 --padding 2 --thr 1 --sampling 0.961270' returned non-zero exit status 1.
[31mProtocol failed: Command ' mpirun -np 8  `which xmipp_mpi_reconstruct_fourier_accel`   -i Runs/008120_XmippProtValidateOverfitting/extra/Nfraction_alignment00_00_00.xmd  -o Runs/008120_XmippProtValidateOverfitting/extra/Nfraction00_00_00.vol --sym c2 --max_resolution 0.500 --padding 2 --thr 1 --sampling 0.961270' returned non-zero exit status 1.[0m



Any ideas?


Thank you

Sincerely,
Dmitry