Dear Sjors,
Tried this, does not show any obvious errors.
I will try latest commit that Takanori fixed and see if ctfrefine lists
the culprit file.
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 15/01/19 10:29, Sjors Scheres wrote:
> 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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>>>>
>>>>
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