Re: [scipion-users] Xmipp viewer issue

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Hi Erik,

It looks like 'which relion_refine_mpi' returns  nothing. Do you have a
correct RELION_HOME set in config file? Did you try running relion with mpi
outside of scipion?

On Thu, Jul 12, 2018, 12:04 Erik Župa <eri...@gm...> wrote:

> I solved the problem of particle extraction window. It was wrong Java
> path. However, my relion 2D classification is not working, Scipion is
> showing  this Error
>
> Erik Zupa
>
> 00021:   mpirun: Error: unknown option "--tau2_fudge"
> 00022:   Type 'mpirun --help' for usage.
> 00023:   Traceback (most recent call last):
> 00024:     File
> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
> line 182, in run
> 00025:       self._run()
> 00026:     File
> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
> line 228, in _run
> 00027:       resultFiles = self._runFunc()
> 00028:     File
> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
> line 224, in _runFunc
> 00029:       return self._func(*self._args)
> 00030:     File
> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/em/packages/relion/protocol_base.py",
> line 789, in runRelionStep
> 00031:       self.runJob(self._getProgram(), params)
> 00032:     File
> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
> line 1077, in runJob
> 00033:       self._stepsExecutor.runJob(self._log, program, arguments,
> **kwargs)
> 00034:     File
> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/executor.py",
> line 56, in runJob
> 00035:       env=env, cwd=cwd)
> 00036:     File
> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/utils/process.py",
> line 51, in runJob
> 00037:       return runCommand(command, env, cwd)
> 00038:     File
> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/utils/process.py",
> line 65, in runCommand
> 00039:       check_call(command, shell=True, stdout=sys.stdout,
> stderr=sys.stderr, env=env, cwd=cwd)
> 00040:     File
> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/lib/python2.7/subprocess.py",
> line 540, in check_call
> 00041:       raise CalledProcessError(retcode, cmd)
> 00042:   CalledProcessError: Command 'mpirun -np 3 -bynode  `which
> relion_refine_mpi` --tau2_fudge 2 --scale  --iter 25 --norm
> --memory_per_thread 2 --ctf  --offset_range 5.0 --oversampling 1 --o
> Runs/003210_ProtRelionClassify2D/extra/relion --i
> Runs/003210_ProtRelionClassify2D/input_particles.star --particle_diameter
> 210.0 --K 3 --psi_step 10.0 --ctf_phase_flipped  --flatten_solvent
> --zero_mask  --offset_step 2.0 --angpix 3.0  --j 1' returned non-zero exit
> status 213
> 00043:   Protocol failed: Command 'mpirun -np 3 -bynode  `which
> relion_refine_mpi` --tau2_fudge 2 --scale  --iter 25 --norm
> --memory_per_thread 2 --ctf  --offset_range 5.0 --oversampling 1 --o
> Runs/003210_ProtRelionClassify2D/extra/relion --i
> Runs/003210_ProtRelionClassify2D/input_particles.star --particle_diameter
> 210.0 --K 3 --psi_step 10.0 --ctf_phase_flipped  --flatten_solvent
> --zero_mask  --offset_step 2.0 --angpix 3.0  --j 1' returned non-zero exit
> status 213
>
> On Tue, Jul 10, 2018 at 12:01 PM, Pablo Conesa <pc...@cn...>
> wrote:
>
>> is java in your path?
>>
>> what happens if you type in the "console/terminal":
>>
>> java -version
>>
>>
>>
>> On 09/07/18 14:39, David Maluenda wrote:
>>
>> Ouch.. strange..
>>
>> What appears as Output for the Xmipp-ExtractParticles? Could the output
>> set be empty?
>> The summary tab (in the scipion GUI) should display:
>>
>> *Name-of-the-protocol* -> outputParticles            SetOfParticles (* #
>> items*, ** x **, **.* A/px )
>>
>> Then, the number of items # is bigger than 0?
>>
>>  <http://ucm.es/>
>>
>> *_____ Dr. David Maluenda Niubó*
>> dma...@cn... - (+34) 619 029 310
>> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
>> BioComputing Unit <http://biocomputingunit.es/>
>>
>> This email message and any documents attached to it may contain
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>>
>>
>>
>> On Mon, Jul 9, 2018 at 1:23 PM Erik Župa <eri...@gm...> wrote:
>>
>>> Hi David,
>>>
>>> I am not receiving any error messages from Scipion after the command.
>>> However, there is no new window popping out after the command.
>>>
>>> Erik Zupa
>>>
>>>
>>> On Mon, Jul 9, 2018 at 12:24 PM, David Maluenda <dma...@cn...>
>>> wrote:
>>>
>>>> Hi Erik,
>>>>
>>>> This is the command that Scipion launch to open the viewer and it looks
>>>> fine.. so, it should open a window with the particles...
>>>>
>>>> Is there any error message after the command that you are reporting?
>>>>
>>>> Thanks!
>>>>
>>>>  <http://ucm.es/>
>>>>
>>>> *_____ Dr. David Maluenda Niubó*
>>>> dma...@cn... - (+34) 619 029 310
>>>> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
>>>> BioComputing Unit <http://biocomputingunit.es/>
>>>>
>>>> This email message and any documents attached to it may contain
>>>> confidential or legally protected material and are intended solely for the
>>>> use of the individual or organization to whom they are addressed. We remind
>>>> you that if you are not the intended recipient of this email message or the
>>>> person responsible for processing it, then you are not authorized to read,
>>>> save, modify, send, copy or disclose any of its contents. If you have
>>>> received this email message by mistake, we kindly ask you to inform the
>>>> sender of this and to eliminate both the message and any attachments it
>>>> carries from your account. Thank you for your collaboration.
>>>>
>>>>
>>>>
>>>> On Mon, Jul 9, 2018 at 11:39 AM Erik Župa <eri...@gm...> wrote:
>>>>
>>>>> Hello colleagues,
>>>>>
>>>>>
>>>>> I have problem to analyze results of extracting of particles. I
>>>>> successfully ran xmipp3- extract particles. However, I cannot analyze
>>>>> results because everytime I try, Scipion come with something like this:
>>>>>
>>>>>
>>>>> java -Xmx2g -d64
>>>>> -Djava.library.path=/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/lib
>>>>> -Dplugins.dir=/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/external/imagej/plugins
>>>>> -cp
>>>>> /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-3.b10.fc26.x86_64/lib/*:/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/external/imagej/*:/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/java/lib/*
>>>>> xmipp.viewer.scipion.ScipionViewer -i
>>>>> "Runs/002809_XmippProtExtractParticles/particles.sqlite" --visible id
>>>>> enabled _index _filename _xmipp_zScore _xmipp_cumulativeSSNR _sampling
>>>>> _ctfModel._defocusU _ctfModel._defocusV _ctfModel._defocusAngle
>>>>> _transform._matrix --order id enabled _index _filename _xmipp_zScore
>>>>> _xmipp_cumulativeSSNR _sampling _ctfModel._defocusU _ctfModel._defocusV
>>>>> _ctfModel._defocusAngle _transform._matrix --render _filename --sortby
>>>>> _xmipp_zScore asc --scipion 55971 2856
>>>>>
>>>>>
>>>>> I am thankful for any help.
>>>>>
>>>>> Erik Zupa
>>>>>
>>>>> CEITEC Brno Czech Republic
>>>>>
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>>>>>
>>>>
>>>
>>
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Re: [scipion-users] Xmipp viewer issue

Image processing framework to integrate EM software packages.

Re: [scipion-users] Xmipp viewer issue