I think this can also happen if you accidentally over-write your scratch copy of your particles by running another relion refinement in the same scratch folder?
D

Sent from my iPhone

> On 10 Dec 2018, at 11:31, Sjors Scheres <[log in to unmask]> wrote:
> 
> Hi Chris,
> 
> 
> This then should not happen. Did you perhaps combine STAR files from
> previous extractions, and then overwrite the stacks with a new
> extraction with fewer particles (perhaps by increasing the box size, so
> some fell off the edge)? Or did you perhaps script around the star files
> generated by the relion workflow? I would probably try to track back
> where
> [log in to unmask]
> entry in the STAR file originally came from.
> 
> 
> HTH,
> Sjors
> 
> 
> 
>> On 12/07/2018 04:24 PM, Chris Richardson wrote:
>> 
>> This may not be the case for you, but in the past when I have seen the
>> error "Image number # exceeds stack size of #" it is because
>> micrographs have been imported from outside the Relion project directory.
>> 
>> 
>> If the micrographs.star file has relative paths to micrographs and
>> contains '..' in the path, this can cause Relion to create directories
>> outside/above the job directory.  For example, in an Extract job, the
>> Micrographs directory will end up inside Extract rather than inside
>> Extract/job0xx.  This then leads to that rather cryptic error message.
>> 
>> 
>> This might not be the only cause of this error, but it's where I look
>> first when one of our group has the problem.
>> 
>>  
>> 
>> Regards,
>> 
>> 
>> Chris
>> 
>> 
>> 
>> ------------------------------------------------------------------------
>> *From:* Collaborative Computational Project in Electron
>> cryo-Microscopy <[log in to unmask]> on behalf of Dienemann,
>> Christian <[log in to unmask]>
>> *Sent:* 07 December 2018 15:39
>> *To:* [log in to unmask]
>> *Subject:* [ccpem] image number exceeds stack size
>>  
>> 
>> Hi,
>> 
>>  
>> 
>> I encountered a funky error in Relion 3. I attempted to refine a large
>> particle data set with ~700000 ptcls and got the following error:
>> 
>>  
>> 
>> in: /home/emuser/emtools/relion-3.0_beta/src/rwMRC.h, line 191
>> 
>> === Backtrace  ===
>> 
>> /home/emuser/emtools/relion-3.0_beta/build/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41)
>> [0x43f211]
>> 
>> /home/emuser/emtools/relion-3.0_beta/build/bin/relion_refine_mpi(_ZN5ImageIdE7readMRCElbRK8FileName+0x88c)
>> [0x4756bc]
>> 
>> /home/emuser/emtools/relion-3.0_beta/build/bin/relion_refine_mpi(_ZN5ImageIdE5_readERK8FileNameR13fImageHandlerblbb+0x17b)
>> [0x47705b]
>> 
>> /home/emuser/emtools/relion-3.0_beta/build/bin/relion_refine_mpi(_ZN11MlOptimiser41calculateSumOfPowerSpectraAndAverageImageER13MultidimArrayIdEb+0x4a0)
>> [0x59ddb0]
>> 
>> /home/emuser/emtools/relion-3.0_beta/build/bin/relion_refine_mpi(_ZN14MlOptimiserMpi41calculateSumOfPowerSpectraAndAverageImageER13MultidimArrayIdE+0x23)
>> [0x457cd3]
>> 
>> /home/emuser/emtools/relion-3.0_beta/build/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x9f4)
>> [0x45f1d4]
>> 
>> /home/emuser/emtools/relion-3.0_beta/build/bin/relion_refine_mpi(main+0xb0b)
>> [0x42cc5b]
>> 
>> /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f03e4e8fb35]
>> 
>> /home/emuser/emtools/relion-3.0_beta/build/bin/relion_refine_mpi()
>> [0x42ffef]
>> 
>> ==================
>> 
>> ERROR:
>> 
>> readMRC: Image number 164 exceeds stack size 163 of image
>> [log in to unmask]
>> 
>>  
>> 
>> I checked the particle stack and it only contains 163 images. The star
>> file also only contains 163 entries for that particle stack (last is
>> [log in to unmask]).
>> 
>>  
>> 
>>  
>> 
>> Best,
>> 
>> Chris
>> 
>>  
>> 
>>  
>> 
>> Christian Dienemann
>> Max-Planck-Institute for Biophysical Chemistry
>> Department of Molecular Biology / Cramer lab
>> Am Fassberg 11
>> 37077 Göttingen, Germany
>> +49-551-201-2819
>> 
>>  
>> 
>> 
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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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