Hi Takanori,

>Is this the first time CtfRefine is performed on this dataset?
Yes

>Was it successful on this machine with other datasets?
Yes

> Does it work if you refine only one of them?
No

> What happens if you reduce the number of MPI processes and threads? (Just in case you ran out of memory)?
Fails with 1 mpi and 1 thread

>Does it work on a smaller subset of the dataset?
No

Thank you,
Yaroslav

-----Original Message-----
From: Takanori Nakane <[log in to unmask]> 
Sent: Thursday, April 11, 2024 6:26 PM
To: Tsybovsky, Yaroslav (NIH/NCI) [C] <[log in to unmask]>
Cc: [log in to unmask]
Subject: [EXTERNAL] Re: [ccpem] relion 5: relion_ctf_refine segmentation fault

Hi,

 > The previous steps were pretty standard.

Is this the first time CtfRefine is performed on this dataset? Was it successful on this machine with other datasets?

 > estimate anisotropic magnification or refine  > per-particle defocus

Does it work if you refine only one of them?

What happens if you reduce the number of MPI processes and threads? (Just in case you ran out of memory)

Does it work on a smaller subset of the dataset?
(Try using particles from only one micrograph) Your dataset might contain one or a few offending particles.

Best regards,

Takanori Nakane

On 4/11/24 23:35, Tsybovsky, Yaroslav (NIH/NCI) [C] wrote:
> Hello everybody,
>
> I have relion_ctf_refine from relion 5.0-beta-o-commit-90d239 
> seg-faulting when trying to estimate anisotropic magnification or 
> refine per-particle defocus. When run from GUI, the output stops after 
> the progress bar appears. When the command (from "Check command") is 
> run from command line, there is a "Segmentation fault (core dumped)"
> immediately after the progress bar appears. The command itself is:
>
> `which relion_ctf_refine` --i Refine3D/job045/run_data.star --f 
> PostProcess/job046/postprocess.star --o CtfRefine/job047/ --fit_aniso 
> --kmin_mag 30 --only_do_unfinished  --j 32  --pipeline_control 
> CtfRefine/job047/
>
> The previous steps were pretty standard. Is this a known problem?
>
> Thank you,
>
> Yaroslav
>
> Yaroslav Tsybovsky, Ph.D. (contractor)
>
> Principal Scientist & Head
>
> Vaccine Research Center Electron Microscopy Unit
>
> Frederick National Laboratory for Cancer Research
>
> Leidos Biomedical Research, Inc.
>
> Post Office Box B
>
> Frederick, Maryland 21702
>
> Phone: 301-846-7550
>
>
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