Hi Leo,
Can you do something like relion_image_handler --stats --i input.star,
where the star file points to all the input images for your job? That's
usually a good way to find corrupt files.
HTH,
Sjors
On 01/09/2019 12:31 PM, Leonid Sazanov wrote:
> Dear Sjors,
>
> As I mentioned, error messages looked a bit different each time, so I
> did not post them initially.
>
> Now I noticed that all of them eventually trace back to the same line
> in code, related to MRC file read/write:
>
> in: /localhome/schloegl/src/relion-3.0-beta/src/rwMRC.h, line 191
> terminate called after throwing an instance of 'RelionError'
>
> This is the example command:
>
> `which relion_ctf_refine` --i Refine3D/job184/run_data.star --f
> PostProcess/job196/postprocess.star --m1
> Refine3D/job184/run_half1_class001_unfil.mrc --m2
> Refine3D/job184/run_half2_class001_unfil.mrc --mask
> MaskCreate/job156/mask_156.mrc --o CtfRefine/job226/ --kmin_defocus 30
> --fit_defocus --range 2000 --fit_beamtilt --kmin_tilt 30
> --only_do_unfinished --j 8
>
> With this set of particles (~30K, ~3.8 A resolution) CtfRefine always
> fails, but with another set from the same micrographs (170K, 3.9 A
> resolution) the same type of command works.
>
> I double checked that all files are in place and there are no issues
> with permissions, so I am not sure why MRC file read/writing fails.
>
> Thanks,
>
> Leo
>
> Prof. Leonid Sazanov
> IST Austria
> Am Campus 1
> A-3400 Klosterneuburg
> Austria
>
> Phone: +43 2243 9000 3026
> E-mail: [log in to unmask]
>
> On 07/01/19 09:04, Sjors Scheres wrote:
>> Dear Leo,
>>
>> I'm afraid this message does not provide a good starting point for a
>> follow-up investigation on our side. The below is not only for you, but
>> also for the community.
>>
>> When reporting errors, it is very useful for us to:
>> 1) know the exact command line arguments
>> 2) know the exact error
>> 3) know when that error occurs and when not
>> 4) (most useful) have a small test case you could share with us that
>> quickly and reproducibly leads to the error.
>>
>> In such cases we can relatively quickly find the error. Otherwise, it
>> may
>> take a long time...
>>
>> HTH,
>> Sjors
>>
>>
>>> Hi, recently using Relion3 build from 04 Dec with CtfRefine I
>>> constantly
>>> get cryptic errors which are different depending on whether I use
>>> several
>>> mpi and several threads or one mpi and several threads or even if
>>> just 1
>>> mpi and 1 thread. Larger set of particles from the same set of images
>>> works fine, so that is really puzzling.
>>> Any info on what may help highly appreciated.
>>> Thanks!
>>>
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>>
>
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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