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

[Grigory S. <sha...@gm...>]

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...

On Mon, Nov 7, 2016 at 4:30 PM, Carlos Oscar Sorzano <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_XmippProtCTFCorrec
> tWiener2D/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...
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