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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