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Subject:

Re: Motioncorr error in Relion3

From:

Takanori Nakane <[log in to unmask]>

Reply-To:

Takanori Nakane <[log in to unmask]>

Date:

Wed, 23 Jan 2019 15:12:16 -0000

Content-Type:

text/plain

Parts/Attachments:
Parts/Attachments

text/plain (254 lines) 

Hi,

> Sep21_15.06.10.tif: LZWDecode: Not enough data at scanline 4140 (short 14
> bytes).

This suggests that this movie is truncated. Please exclude this movie.

Best regards,

Takanori Nakane

> Hi,
>
>     I also had a problem to run Relion's implement MotionCorr. The job
> crashes at certain micrograph. I follow the suggestion to check the
> micrographs, and it gave me the following error message:
>
> [sliou@loginnode4 Movies]$ relion_image_handler --stats --i
> Sep21_15.06.10.tif
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365515
> stddev= 0.607 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365277
> stddev= 0.607114 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365279
> stddev= 0.606898 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.364967
> stddev= 0.606614 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365083
> stddev= 0.606924 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365261
> stddev= 0.607006 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.366044
> stddev= 0.608 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365965
> stddev= 0.608157 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365091
> stddev= 0.607326 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365651
> stddev= 0.607914 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365797
> stddev= 0.607972 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365518
> stddev= 0.607778 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365468
> stddev= 0.60778 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.36558
> stddev= 0.607877 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365938
> stddev= 0.608182 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365303
> stddev= 0.607596 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365148
> stddev= 0.607567 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365756
> stddev= 0.607997 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365545
> stddev= 0.607891 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365981
> stddev= 0.60824 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.366101
> stddev= 0.608337 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.366111
> stddev= 0.608388 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365739
> stddev= 0.608065 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365295
> stddev= 0.607655 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365675
> stddev= 0.607963 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.366148
> stddev= 0.608307 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.366061
> stddev= 0.608347 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365572
> stddev= 0.607876 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365725
> stddev= 0.607951 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365771
> stddev= 0.607985 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.366166
> stddev= 0.60841 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365723
> stddev= 0.607981 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365862
> stddev= 0.608092 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365738
> stddev= 0.607942 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.366026
> stddev= 0.608353 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365887
> stddev= 0.608127 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365925
> stddev= 0.608229 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.366154
> stddev= 0.608545 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365982
> stddev= 0.608195 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365588
> stddev= 0.607891 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.366119
> stddev= 0.608331 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365645
> stddev= 0.607792 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.36562
> stddev= 0.607913 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365396
> stddev= 0.607789 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.366024
> stddev= 0.608213 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365976
> stddev= 0.608201 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.366195
> stddev= 0.608284 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365432
> stddev= 0.607696 minval= 0 maxval= 15
> [log in to unmask] : (x,y,z,n)= 7676 x 7420 x 1 x 1 ; avg= 0.365581
> stddev= 0.607965 minval= 0 maxval= 15
> Sep21_15.06.10.tif: LZWDecode: Not enough data at scanline 4140 (short 14
> bytes).
> Segmentation fault
>
> The last two lines are definitely the error message I saw in MotionCorr.
> Could you please help me to see if anything wrong in this micrograph?
>
> Best,
> Shu-hao
>
> ________________________________________
> From: Collaborative Computational Project in Electron cryo-Microscopy
> [[log in to unmask]] on behalf of Takanori Nakane
> [[log in to unmask]]
> Sent: Wednesday, November 28, 2018 2:55 AM
> To: [log in to unmask]
> Subject: Re: [ccpem] Motioncorr error in Relion3
>
> Hi,
>
>  > I'm having trouble when running morioncorr in relion3.
>
> Are you running UCSF MotionCor2, or RELION's implementation?
>
>  > It is the first time I saw this, and motioncorr 2 worked perfectly
> for all of my rest dataset.
>
> For successful datasets, did you run MotionCor2 from RELION 3's GUI?
> Or did you run outside RELION?
>
>  > 18jan10d_DHXOB_00022gr_00027sq_v02_00006hln_v01_00005enn.frames.tif
>
> Is this file located just under the project directory? Probably not.
> Why is the path missing?
>
>  > However, I checked very carefully, and it is really there.
>
> Please run 'relion_image_handler --stats --i
> 18jan10d_DHXOB_00022gr_00027sq_v02_00006hln_v01_00005enn.frames.tif'
> to make sure it is redable.
>
> Best regards,
>
> Takanori Nakane
>
> On 2018/11/27 23:23, Da Cui wrote:
>> Hi,
>>    I'm having trouble when running morioncorr in relion3. It is the
>> first time I saw this, and motioncorr 2 worked perfectly for all of
>> my rest dataset.
>>    Below is the error message:
>>   in: /programs/x86_64-linux/relion/3.0_beta_cu8.0/src/image.h, line 174
>> in: /programs/x86_64-linux/relion/3.0_beta_cu8.0/src/image.h, line 174
>> === Backtrace  ===
>> === Backtrace  ===
>> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_run_motioncorr_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41)
>> [0x49a9c1]
>> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_run_motioncorr_mpi(_ZN13fImageHandler8openFileERK8FileNamei+0xc5d)
>> [0x445a2d]
>> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_run_motioncorr_mpi(_ZN10Micrograph8setMovieE8FileNameS0_d+0x327)
>> [0x476057]
>> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_run_motioncorr_mpi(_ZN10MicrographC2E8FileNameS0_d+0x22b)
>> [0x476cbb]
>> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_run_motioncorr_mpi(_ZN19MotioncorrRunnerMpi3runEv+0x274)
>> [0x471504]
>> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_run_motioncorr_mpi(main+0x3b)
>> [0x4205fb]
>> /lib64/libc.so.6(__libc_start_main+0xf5) [0x2aaab9682af5]
>> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_run_motioncorr_mpi()
>> [0x420cb1]
>> ==================
>> ERROR:
>> Cannot read file
>> 18jan10d_DHXOB_00015gr_00023sq_v02_00003hln_v01_00005enn.frames.tif It
>> does not exist
>> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_run_motioncorr_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41)
>> [0x49a9c1]
>> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_run_motioncorr_mpi(_ZN13fImageHandler8openFileERK8FileNamei+0xc5d)
>> [0x445a2d]
>> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_run_motioncorr_mpi(_ZN10Micrograph8setMovieE8FileNameS0_d+0x327)
>> [0x476057]
>> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_run_motioncorr_mpi(_ZN10MicrographC2E8FileNameS0_d+0x22b)
>> [0x476cbb]
>> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_run_motioncorr_mpi(_ZN19MotioncorrRunnerMpi3runEv+0x274)
>> [0x471504]
>> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_run_motioncorr_mpi(main+0x3b)
>> [0x4205fb]
>> /lib64/libc.so.6(__libc_start_main+0xf5) [0x2aaab9682af5]
>> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_run_motioncorr_mpi()
>> [0x420cb1]
>> ==================
>> ERROR:
>> Cannot read file
>> 18jan10d_DHXOB_00022gr_00027sq_v02_00006hln_v01_00005enn.frames.tif It
>> does not exist
>> [node004:19698] 1 more process has sent help message help-mpi-api.txt /
>> mpi-abort
>> [node004:19698] Set MCA parameter "orte_base_help_aggregate" to 0 to see
>> all help / error messages
>>
>>
>> It says a file doesn't exist. However, I checked very carefully, and it
>> is really there.
>> Can anyone please help me what happened? Thank you so much.
>> And this is the command I run: "`which relion_run_motioncorr_mpi` --i
>> Import/job190/movies.star --o MotionCorr/job193/ --first_frame_sum 1
>> --last_frame_sum 0 --use_own  --j 1 --bin_factor 1 --bfactor 150
>> --angpix 1.07 --voltage 300 --dose_per_frame 0.8 --preexposure 0
>> --patch_x 5 --patch_y 5 --gainref
>> references_18jan10/17dec28c_28113917_01_3838x3710_norm_0_mod.mrc
>> --gain_rot 0 --gain_flip 0 --dose_weighting  --save_noDW"
>>
>> Best wishes,
>>        Da
>>
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