Re: [scipion-users] Error running relion

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

Hi Dmitry,

you are looking at a wrong tab, check run.stderr. Also, are you
running relion 3.1?

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 Mon, Sep 27, 2021 at 12:18 PM Dmitry Semchonok <Sem...@gm...>
wrote:

> Dear Grigory & colleagues,
>
> Error running updated relion plugin.
>
>
> Any ideas?
>
> Thank you
>
> Sincerely,
> Dmitry
>
>
>
>
> File 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't existFile
> 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't exist00001:
>  Logging configured. STDOUT -->
> Runs/004970_ProtRelionClassify2D/logs/run.stdout , STDERR -->
> Runs/004970_ProtRelionClassify2D/logs/run.stderr
> 00002:   RUNNING PROTOCOL -----------------
> 00003:   Protocol starts
> 00004:   Hostname: localhost4.localdomain4
> 00005:   PID: 99422
> 00006:   pyworkflow: 3.0.17
> 00007:   plugin: relion
> 00008:   plugin v: 4.0b2
> 00009:   currentDir:
> /home/user/Data/ScipionUserData/projects/Quentin__august__PSI
> 00010:   workingDir: Runs/004970_ProtRelionClassify2D
> 00011:   runMode: Continue
> 00012:             MPI: 6
> 00013:         threads: 4
> 00014:    Starting at step: 1
> 00015:    Running steps
> 00016:   STARTED: convertInputStep, step 1, time 2021-09-27 13:14:18.891805
> 00017:   Converting set from 'Runs/001948_ProtUserSubSet/particles.sqlite'
> into 'Runs/004970_ProtRelionClassify2D/input_particles.star'
> 00018:   convertBinaryFiles: creating soft links.
> 00019:      Root: Runs/004970_ProtRelionClassify2D/extra/input ->
> Runs/001072_ProtRelionExtractParticles/extra
> 00020:   FINISHED: convertInputStep, step 1, time 2021-09-27
> 13:14:20.274397
> 00021:   STARTED: runRelionStep, step 2, time 2021-09-27 13:14:20.279078
> 00022:    mpirun -np 6  `which relion_refine_mpi` --i
> Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter
> 346 --ctf  --zero_mask  --K 24 --norm  --scale  --o
> Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1
> --flatten_solvent  --tau2_fudge 2.0 --iter 25 --offset_range 5.0
> --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc  --pool 3
> --gpu   --j 4
> 00023:   Protocol failed: Command ' mpirun -np 6  `which
> relion_refine_mpi` --i
> Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter
> 346 --ctf  --zero_mask  --K 24 --norm  --scale  --o
> Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1
> --flatten_solvent  --tau2_fudge 2.0 --iter 25 --offset_range 5.0
> --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc  --pool 3
> --gpu   --j 4' returned non-zero exit status 213.
> 00024:   FAILED: runRelionStep, step 2, time 2021-09-27 13:14:20.303854
> 00025:   *** Last status is failed
> 00026:   ------------------- PROTOCOL FAILED (DONE 2/3)