Motion Correction failed.

A same error as PeterXTH posted in 2018, "Motion Correction of Relion 3.0 for Super-resolution Krios data #339

Our movies work well with MotionCorr2 and Cryosparc Motion Correction but show a very large error (above 20 pixels) for patch alignment in RELION. I have run a previous job, the old movies still work well in RELION (K3, with super resolution pixel 0.55) (this indicates that it is not the RELION installation problem). And the new dataset (with super resolution pixel 0.259) succeed in full frame alignment and failed in patch alignment (Both failed in RELION 3.0, 4.0). So, I guess the jobs failed because a relative lower signal to noise ratio. I have changed to larger patches (5X4,4X3,3X3), and it do not work neither.

Is there any way to get rid of this problem?

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Describe your problem

Please write a clear description of what the problem is. Data processing questions should be posted to the CCPEM mailing list, not here. DO NOT cross post a same question to multiple issues and/or many mailing lists (CCPEM, 3DEM, etc).

Environment:

OS: [e.g. Ubuntu 16.04 LTS]
MPI runtime: [e.g. OpenMPI 2.0.1]
RELION version [e.g. RELION-3.1-devel-commit-6ba935 (please see the title bar of the GUI)]
Memory: [e.g. 128 GB]
GPU: [e.g. GTX 1080Ti]

Dataset:

Box size: [e.g. 256 px]
Pixel size: [e.g. 0.9 Å/px]
Number of particles: [e.g. 150,000]
Description: [e.g. A tetrameric protein of about 400 kDa in total]

Job options:

Type of job: [e.g. Refine3D]
Number of MPI processes: [e.g. 4]
Number of threads: [e.g. 6]

Full command (see note.txt in the job directory):

`which relion_refine_mpi` --o Refine3D/job019/run --auto_refine --split_random_halves --i CtfRefine/job018/particles_ctf_refine.star --ref PostProcess/job001/postprocess.mrc --firstiter_cc --ini_high 12 --dont_combine_weights_via_disc --scratch_dir /ssd --pool 3 --pad 2  --ctf --ctf_corrected_ref --particle_diameter 142 --flatten_solvent --zero_mask --solvent_mask Result-by-Rado/run_class001_mask_th0.01_ns3_ngs7_box400.mrc --solvent_correct_fsc  --oversampling 1 --healpix_order 3 --auto_local_healpix_order 4 --offset_range 5 --offset_step 2 --sym O --low_resol_join_halves 40 --norm --scale  --j 8 --gpu "" --keep_scratch --pipeline_control Refine3D/job019/

Error message:

Please cite the full error message as the example below.

A line in the STAR file contains fewer columns than the number of labels. Expected = 3 Found = 2
Error in line: 0 0.0
in: /prog/relion-devel-lmb/src/metadata_table.cpp, line 966
=== Backtrace  ===
/prog/relion-devel-lmb/bin/relion_motion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x42e981]
/prog/relion-devel-lmb/bin/relion_motion_refine_mpi(_ZN13MetaDataTable12readStarLoopERSt14basic_ifstreamIcSt11char_traitsIcEEPSt6vectorI8EMDLabelSaIS6_EESsb+0xedd) [0x4361ad]
/prog/relion-devel-lmb/bin/relion_motion_refine_mpi(_ZN13MetaDataTable8readStarERSt14basic_ifstreamIcSt11char_traitsIcEERKSsPSt6vectorI8EMDLabelSaIS8_EESsb+0x580) [0x436f10]
/prog/relion-devel-lmb/bin/relion_motion_refine_mpi(_ZN10Micrograph4readE8FileNameb+0x5a3) [0x454bb3]
/prog/relion-devel-lmb/bin/relion_motion_refine_mpi(_ZN10MicrographC2E8FileNameS0_d+0x2e3) [0x4568b3]
/prog/relion-devel-lmb/bin/relion_motion_refine_mpi(_ZN17MicrographHandler14isMoviePresentERK13MetaDataTableb+0x180) [0x568280]
/prog/relion-devel-lmb/bin/relion_motion_refine_mpi(_ZN17MicrographHandler17cullMissingMoviesERKSt6vectorI13MetaDataTableSaIS1_EEi+0xe6) [0x568dc6]
/prog/relion-devel-lmb/bin/relion_motion_refine_mpi(_ZN13MotionRefiner4initEv+0x56f) [0x49e1ff]
/prog/relion-devel-lmb/bin/relion_motion_refine_mpi(main+0x31) [0x42a5e1]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2b7ac026e495]
/prog/relion-devel-lmb/bin/relion_motion_refine_mpi() [0x42b3cf]
==================

3dem / relion

Motion Correction failed. #970