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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