Re: [scipion-users] Xmipp viewer issue

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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
> confidential or legally protected material and are intended solely for the
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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