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--- | ||
name: Bug report | ||
about: Report a problem | ||
title: '' | ||
labels: '' | ||
assignees: '' | ||
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--- | ||
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This is a template for asking questions and reporting bugs. Please fill in as much information as you can. | ||
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**Describe your problem** | ||
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Please write a clear description of what the problem is. | ||
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**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] | ||
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**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] | ||
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**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/ | ||
``` | ||
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**Error message:** | ||
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Please cite the *full* error message as the example below. | ||
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``` | ||
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] | ||
================== | ||
``` |