Re: [scipion-users] Error running relion

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

You can see the version via *scipion config -p relion*

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 12:44 PM Dmitry Semchonok <Sem...@gm...>
wrote:

> Dear Grigory,
>
> Sorry, but how to verify the version?
>
> I the plugin I see scipion-em-relion
> Relion-3.1.3
>
>
> Shall I also update for relion-4.0?
>
> Sincerely,
>
> Dmitry
>
>
>
> On 27. Sep 2021, at 13:40, Grigory Sharov <sha...@gm...>
> wrote:
>
> 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)
>
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