From dab3bd4183a0db528fd9f9cc779bb34b81a1139e Mon Sep 17 00:00:00 2001 From: biochem_fan Date: Thu, 10 Oct 2019 11:40:24 +0100 Subject: [PATCH] Create a bug-report template --- .github/ISSUE_TEMPLATE/bug_report.md | 59 ++++++++++++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 .github/ISSUE_TEMPLATE/bug_report.md diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md new file mode 100644 index 000000000..1ada1fa38 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -0,0 +1,59 @@ +--- +name: Bug report +about: Report a problem +title: '' +labels: '' +assignees: '' + +--- + +This is a template for asking questions and reporting bugs. Please fill in as much information as you can. + +**Describe your problem** + +Please write a clear description of what the problem is. + +**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] +================== +```