Re: [scipion-users] Relion 3D initial model failiure

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

Dear Kyrylo,

while it seems to be not a scipion problem, you could run a test first:

scipion3 tests relion.tests.test_protocols_3d.TestRelionInitialModel

If that fails, it may be that your relion/mpi installation is not working.

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, Nov 24, 2022 at 3:13 PM Bisikalo, Kyrylo <
kyr...@he...> wrote:

> Hello,
>
>
>
> I have been trying to process a small dataset (~800 particles), but the 3D
> initial model keeps failing mid-run. It displays the following error:
> “Protocol failed: Command ' relion_refine --i
> Runs/000899_ProtRelionInitialModel/input_particles.star --particle_diameter
> 682 --ctf  --zero_mask  --o Runs/000899_ProtRelionInitialModel/extra/relion
> --oversampling 1 --pad 1 --tau2_fudge 3.0 --flatten_solvent  --sym i2
> --iter 150 --grad  --K 1 --denovo_3dref  --healpix_order 1 --offset_range 6
> --offset_step 2 --auto_sampling  --dont_combine_weights_via_disc
> --preread_images  --pool 3 --gpu   --j 2' died with <Signals.SIGSEGV: 11>.”
>
>
>
> What can be done to amend this?
>
> I have attached the log files to this email.
>
>
>
> Faithfully yours,
>
> Kyrylo Bisikalo
>
> Erasmus Mundus Joint Master’s Degree program
>
> “Advanced Spectroscopy in Chemistry”
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