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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