Re: [scipion-users] errors running xmipp3 - ctf_correct_wiener2d & xmipp3 - reconstruct significant

[Carlos O. S. <co...@cn...>]

Dear all,

reconstruct_significant internally multiplies the significance by the 
symmetry number (this is done to let symmetric particles to have the 
same number of chances as non-symmetric). If you start with 0.2, then 
0.2*12=2.4>1, which is not a valid significance value. In this case, you 
may want to start with 0.98 to 0.999.

Kind regards, Carlos Oscar


On 07/11/2016 16:48, Grigory Sharov wrote:
> Hi Dmitry,
>
> sorry I didn't look carefully first time.
>
> I guess Carlos Oscar can help you with the error with alpha values in 
> significant protocol. I have attached the log files you sent me.
>
>     [32mxmipp_reconstruct_significant -i
>     Runs/001412_XmippProtReconstructSignificant/extra/input_classes.xmd
>     --sym d6 --angularSampling 5.000000 --minTilt 0.000000 --maxTilt
>     90.000000 --maxShift -1.000000 --dontReconstruct --angDistance
>     10.000000 --useImed --odir
>     Runs/001412_XmippProtReconstructSignificant/tmp/iter001 --alpha0
>     0.200000 --alphaF 0.200000 --numberOfVolumes 1 [0m
>     Setting iterations to 1 because of --dontReconstruct
>     Input metadata              :
>     Runs/001412_XmippProtReconstructSignificant/extra/input_classes.xmd
>     Output directory            :
>     Runs/001412_XmippProtReconstructSignificant/tmp/iter001
>     Initial significance        : 0.2
>     Final significance          : 0.2
>     Number of iterations        : 1
>     Keep intermediate volumes   : 0
>     Angular sampling            : 5
>     Maximum shift               : -1
>     Minimum tilt                : 0
>     Maximum tilt                : 90
>     Use Imed                    : 1
>     Angular distance            : 10
>     Apply Fisher                : 0
>     Reconstruct                 : 0
>     useForValidation            : 0
>     Symmetry for projections    : d6
>     Number of volumes           : 1
>     [1;31mXMIPP_ERROR 2:  Incorrect argument received [0m
>     [1;31m [1;31mAlpha values are too large: reduce the error such
>     that the error times the symmetry number is smaller than 1 [0m [0m
>     [1;31mFile:
>     software/em/xmipp/libraries/reconstruction/reconstruct_significant.cpp
>     line: 737
>
>
>
>
> Best regards,
> Grigory
>
> --------------------------------------------------------------------------------
> Grigory Sharov, Ph.D.
> Institute of Genetics and Molecular and Cellular Biology
> Integrated Structural Biology Department (CBI)
> 1, rue Laurent Fries
> 67404 Illkirch, France
> tel. 03 69 48 51 00
> e-mail: sh...@ig... <mailto:sh...@ig...>
>
> On Mon, Nov 7, 2016 at 4:30 PM, Carlos Oscar Sorzano <co...@cn... 
> <mailto:co...@cn...>> wrote:
>
>     Dear Dmitry,
>
>     as Grigori says, only with these errors it is hard to say what is
>     going on, is there any other error message?
>
>     Kind regards, Carlos Oscar
>
>
>     On 11/07/16 13:22, Dmitry Semchonok wrote:
>>     Dear colleagues,
>>
>>     I have a problem with running
>>
>>     xmipp3 - ctf_correct_wiener2d
>>     <https://github.com/I2PC/scipion/wiki/XmippProtCTFCorrectWiener2D>:
>>
>>     xmipp3 - reconstruct significant
>>     <https://github.com/I2PC/scipion/wiki/XmippProtReconstructSignificant>:
>>
>>
>>     I faced the following errors:
>>
>>     xmipp3 - ctf_correct_wiener2d
>>     <https://github.com/I2PC/scipion/wiki/XmippProtCTFCorrectWiener2D>:
>>     Protocol failed: Command 'srun  `which
>>     xmipp_mpi_ctf_correct_wiener2d`   -i
>>     Runs/001129_XmippProtCTFCorrectWiener2D/input_particles.xmd -o
>>     Runs/001129_XmippProtCTFCorrectWiener2D/corrected_ctf_particles.stk
>>     --save_metadata_stack
>>     Runs/001129_XmippProtCTFCorrectWiener2D/corrected_ctf_particles.xmd
>>     --pad 2  --wc -1.0  --sampling_rate 2.24' returned non-zero exit
>>     status 127
>>
>>
>>     xmipp3 - reconstruct significant
>>     <https://github.com/I2PC/scipion/wiki/XmippProtReconstructSignificant>
>>     Protocol failed: Command 'srun  `which
>>     xmipp_mpi_reconstruct_significant` -i
>>     Runs/001892_XmippProtReconstructSignificant/extra/input_classes.xmd
>>     --sym c1 --angularSampling 5.000000 --minTilt 0.000000 --maxTilt
>>     90.000000 --maxShift -1.000000 --dontReconstruct --angDistance
>>     10.000000 --useImed --odir
>>     Runs/001892_XmippProtReconstructSignificant/tmp/iter001 --alpha0
>>     0.200000 --alphaF 0.200000 --numberOfVolumes 1' returned non-zero
>>     exit status 127
>>
>>
>>
>>
>>     Any suggestions?
>>
>>     Thank you.
>>
>>     Sincerely,
>>     Dmitry
>>
>>
>>
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>     -- 
>     ------------------------------------------------------------------------
>     Carlos Oscar Sánchez Sorzano                  e-mail:co...@cn... <mailto:co...@cn...>
>     Biocomputing unithttp://biocomp.cnb.csic.es
>     National Center of Biotechnology (CSIC)
>     c/Darwin, 3
>     Campus Universidad Autónoma (Cantoblanco)     Tlf: 34-91-585 4510
>     28049 MADRID (SPAIN)                          Fax: 34-91-585 4506
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>     Intel Xeon Phi processor-based developer platforms. With one year
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-- 
------------------------------------------------------------------------
Carlos Oscar Sánchez Sorzano                  e-mail:   co...@cn...
Biocomputing unit                             http://biocomp.cnb.csic.es
National Center of Biotechnology (CSIC)
c/Darwin, 3
Campus Universidad Autónoma (Cantoblanco)     Tlf: 34-91-585 4510
28049 MADRID (SPAIN)                          Fax: 34-91-585 4506
------------------------------------------------------------------------