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Re: [scipion-users] Relion 3D classification error
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From: Anastasina, M. <mar...@he...> - 2021-09-30 09:12:41
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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...<mailto: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<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Wed, Sep 29, 2021 at 6:07 PM Anastasina, Maria <mar...@he...<mailto: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...<mailto: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...<mailto:gs...@mr...> On Wed, Sep 29, 2021 at 4:08 PM Anastasina, Maria <mar...@he...<mailto: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 > _______________________________________________ > scipion-users mailing list > sci...@li...<mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |
