Re: [scipion-users] Relion 3D classification error

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

Hi,

thank you for sending over the files from the original job. I'm afraid I
will need the
Runs/011346_ProtRelionClassify3D/extra/relion_it025_model.star as well.

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gs...@mr...


On Thu, Sep 30, 2021 at 5:25 PM Anastasina, Maria <
mar...@he...> wrote:

> Hi Grigory,
>
> Thank you for looking into my files. Yes, this job is a continuation of
> another one where 25 iterations were completed, but CreateOutput step
> failed with exactly the same error message. This is why I put 0 iterations
> in the job, hoping that it will just manage to create the output (or was it
> a wrong idea?).
>
> Since the original job with 25 iterations also filed, it seems that the
> source of error is something else, or maybe was a problem with that
> original job that migrated to the next one (sorry if it sounds confusing)?.
> Just in case, I attach here .stderr and .stdout files form the original job
> too. There all 25 iterations were completed, but the CreateOutput failed.
>
> Best,
> Maria
>
>
>
>
>
>
> On 30. Sep 2021, at 11.50, Grigory Sharov <sha...@gm...>
> wrote:
>
> Hello Maria,
>
> srun  `which relion_refine_mpi` --norm  --scale  --o
> Runs/012188_ProtRelionClassify3D/extra/relion --oversampling 1
> --flatten_solvent  --tau2_fudge 4.0 --iter 25 --pad 2 --skip_gridding
>  --healpix_order 4 --offset_range 5.0 --offset_step 2.0 --continue
> Runs/011346_ProtRelionClassify3D/extra/relion_it025_optimiser.star
> --dont_combine_weights_via_disc  --pool 3 --gpu   --j 4
>
> You are running a job that will not do anything, continuing from iteration
> 25 until 25. Did you put 0 in number of iterations in the protocol?
>
> Best regards,
> Grigory
>
>
> --------------------------------------------------------------------------------
> Grigory Sharov, Ph.D.
>
> MRC Laboratory of Molecular Biology,
> Francis Crick Avenue,
> Cambridge Biomedical Campus,
> Cambridge CB2 0QH, UK.
> tel. +44 (0) 1223 267228 <+44%201223%20267228>
> e-mail: gs...@mr...
>
>
> On Wed, Sep 29, 2021 at 6:07 PM Anastasina, Maria <
> mar...@he...> wrote:
>
> Dear Grigory,
>
> Here they go
>
> Best,
> Maria
>
> [masha@puhti-login2 ~]$ scipion3 config -p relion
> Scipion v3.0.8 - Eugenius
> Variables defined by plugin 'relion':
>
> RELION_HOME = /appl/soft/math/scipion/3.0.7/software/em/relion-3.1.1
> RELION_CUDA_LIB =
> /appl/spack/install-tree/gcc-8.3.0/cuda-10.1.168-mrdepn/lib64
>
> These variables can be added/edited in
> '/appl/soft/math/scipion/3.0.7/config/scipion.conf'
>
>
> On 29. Sep 2021, at 18.28, Grigory Sharov <sha...@gm...>
> wrote:
>
> Dear Maria,
>
> could you please
>
> 1) post here the output of "scipion3 config -p relion"
> 2) attach run.stdout and run.stderr files from the failed protocol
>
> Thank you.
>
> Best regards,
> Grigory
>
>
> --------------------------------------------------------------------------------
> Grigory Sharov, Ph.D.
>
> MRC Laboratory of Molecular Biology,
> Francis Crick Avenue,
> Cambridge Biomedical Campus,
> Cambridge CB2 0QH, UK.
> tel. +44 (0) 1223 267228
> e-mail: gs...@mr...
>
>
> On Wed, Sep 29, 2021 at 4:08 PM Anastasina, Maria <
> mar...@he...> wrote:
> >
> > Hello,
> >
> > All my recent Relion 3D classification jobs the I run in Scipion fail at
> CreateOutput step  with the error message "Protocol failed: 'Class3D'
> object has no attribute ‘_rlnClassDistribution’”.
> >
> > Jobs that I ran earlier (e.g. 10 days ago) in identical conditions used
> to finish successfully. I’m not aware of any changes or updates that have
> been done at our HPC server or Scipion installation (we use Scipion 3.0.8).
> >
> > Do you know what could be the reason for this error?
> >
> > Best regards,
> > Maria
> > _______________________________________________
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> > sci...@li...
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