Re: [scipion-users] MonoRes issues

[JOSE L. V. P. <jl...@cn...>]

Dear Chen Sun,

First, thanks for using MonoRes.

Regarding with the error, I would say one of next reasons for this error.

1) MonoRes establish a comparison between signal and noise at  
different frequencies. The mask is used to localize the signal and the  
noise. A possible fail reason is if your volume (or halves) does not  
present noise, in that case, there is nothing to be compared and  
MonoRes cast and error.

2) An alternative is to check your mask, It should be binary, (in next  
release -soon- this condition it is not necessary).

4) If your virus was masked with an spherical mask, please provide the  
radius of that mask. You have to put enable the option mask radius.

I expect that one of this reason will solve your problem, otherwise,  
please write us again, and we go in more detail


Regards

Jose Luis Vilas

Quoting Chen Sun <su...@pu...>:

> Dear all,
>
>
> I am trying to use MonoRes to estimate the local resolution of my  
> virus map (320x320pixel box size). However, it failed more than four  
> times with the same error message which is copied below. Is it a  
> memory issue? I have run it successfully with a smaller map (256x256  
> pixel box size). Do anyone know how to work around this problem?
>
>
> The error message:
>
> Search of resolutions stopped due to mask has been completed
> 00114:   Segmentation fault (core dumped)
> 00115:   Traceback (most recent call last):
> 00116:     File  
> "/net/apps/linux/scipion/1.2/pyworkflow/protocol/protocol.py", line  
> 186, in run
> 00117:       self._run()
> 00118:     File  
> "/net/apps/linux/scipion/1.2/pyworkflow/protocol/protocol.py", line  
> 233, in _run
> 00119:       resultFiles = self._runFunc()
> 00120:     File  
> "/net/apps/linux/scipion/1.2/pyworkflow/protocol/protocol.py", line  
> 229, in _runFunc
> 00121:       return self._func(*self._args)
> 00122:     File  
> "/net/apps/linux/scipion/1.2/pyworkflow/em/packages/xmipp3/protocol_resolution_monogenic_signal.py", line 252, in  
> resolutionMonogenicSignalStep
> 00123:       self.runJob('xmipp_resolution_monogenic_signal', params)
> 00124:     File  
> "/net/apps/linux/scipion/1.2/pyworkflow/protocol/protocol.py", line  
> 1138, in runJob
> 00125:       self._stepsExecutor.runJob(self._log, program,  
> arguments, **kwargs)
> 00126:     File  
> "/net/apps/linux/scipion/1.2/pyworkflow/protocol/executor.py", line  
> 56, in runJob
> 00127:       env=env, cwd=cwd)
> 00128:     File  
> "/net/apps/linux/scipion/1.2/pyworkflow/utils/process.py", line 51,  
> in runJob
> 00129:       return runCommand(command, env, cwd)
> 00130:     File  
> "/net/apps/linux/scipion/1.2/pyworkflow/utils/process.py", line 65,  
> in runCommand
> 00131:       check_call(command, shell=True, stdout=sys.stdout,  
> stderr=sys.stderr, env=env, cwd=cwd)
> 00132:     File  
> "/net/apps/linux/scipion/1.2/software/lib/python2.7/subprocess.py",  
> line 186, in check_call
> 00133:       raise CalledProcessError(retcode, cmd)
> 00134:   CalledProcessError: Command  
> 'xmipp_resolution_monogenic_signal  --vol  
> Runs/000421_ProtImportVolumes/extra/half2.mrc:mrc --vol2  
> Runs/000461_ProtImportVolumes/extra/half1.mrc:mrc --meanVol  
> Runs/000535_XmippProtMonoRes/extra/mean_volume.vol --mask  
> Runs/000501_ProtImportMask/extra/mask.mrc --mask_out  
> Runs/000535_XmippProtMonoRes/extra/output_Mask.vol -o  
> Runs/000535_XmippProtMonoRes/extra/mgresolution.vol --sampling_rate  
> 1.297500 --number_frequencies 50.000000 --minRes 2.000000 --maxRes  
> 5.000000 --volumeRadius 160.000000 --chimera_volume  
> Runs/000535_XmippProtMonoRes/extra/MG_Chimera_resolution.vol --sym i  
> --significance 0.950000 --md_outputdata  
> Runs/000535_XmippProtMonoRes/extra/mask_data.xmd --filtered_volume '  
> returned non-zero exit status 139
> 00135:   Protocol failed: Command 'xmipp_resolution_monogenic_signal  
>  --vol Runs/000421_ProtImportVolumes/extra/half2.mrc:mrc --vol2  
> Runs/000461_ProtImportVolumes/extra/half1.mrc:mrc --meanVol  
> Runs/000535_XmippProtMonoRes/extra/mean_volume.vol --mask  
> Runs/000501_ProtImportMask/extra/mask.mrc --mask_out  
> Runs/000535_XmippProtMonoRes/extra/output_Mask.vol -o  
> Runs/000535_XmippProtMonoRes/extra/mgresolution.vol --sampling_rate  
> 1.297500 --number_frequencies 50.000000 --minRes 2.000000 --maxRes  
> 5.000000 --volumeRadius 160.000000 --chimera_volume  
> Runs/000535_XmippProtMonoRes/extra/MG_Chimera_resolution.vol --sym i  
> --significance 0.950000 --md_outputdata  
> Runs/000535_XmippProtMonoRes/extra/mask_data.xmd --filtered_volume '  
> returned non-zero exit status 139
> 00136:   FAILED: resolutionMonogenicSignalStep, step 2
>
>
> Thanks,
>
> Chen