Describe your problem

After completing the first iteration in a Refine3D job, the job crashes and provides an error that a pair of same helical segments has been found. Prior to this job, an initial 3D model was generated using relion_helix_inimodel2d. That model, along with the particles from the good 2D classes, were used in a 3D classification job to produce 4 classes. 3 of those were chosen, with 1 being used as the reference model for the Refine3D job. I have tried regrouping particles as well as remove duplicates within the subset selection job but haven't found luck with those. Thank you for your help!

Environment:

• OS: Linux 5.15.0
• MPI runtime: OpenMPI 4.1.2
• RELION version RELION-5.0-beta-1-commit-6a43bb
• Memory: 128 GB
• GPU: NVIDIA A6000

Dataset:

• Box size: 320 px
• Pixel size: 0.825 Å/px
• Number of particles: 300,000
• Description: Peptide-based molecules (~13 amino acids covalently bonded) that assemble into long fibrils, roughly 10 nm in diameter

Job options:

• Type of job: Refine3D
• Number of MPI processes: 5
• Number of threads: 4
• Full command :

  `which relion_refine_mpi` --o Refine3D/job081/run --auto_refine --split_random_halves --i Select/job079/particles.star --ref Refine3D/job077/run_class001.mrc --firstiter_cc --trust_ref_size --ini_high 10 --dont_combine_weights_via_disc --pool 30 --pad 2  --ctf --particle_diameter 237 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 3 --auto_local_healpix_order 4 --offset_range 8 --offset_step 2 --sym C1 --low_resol_join_halves 40 --norm --scale  --helix --helical_outer_diameter 125 --helical_nr_asu 3 --helical_twist_initial 1.4 --helical_rise_initial 4.69 --helical_z_percentage 0.3 --sigma_tilt 5 --sigma_psi 3.33333 --sigma_rot 0 --helical_sigma_distance 0.666667 --helical_keep_tilt_prior_fixed --j 4 --gpu ""  --pipeline_control Refine3D/job081/
  

Error message:

Compare # 1 with # 0
in: /opt/relion/relion-5.0-beta-1/src/helix.cpp, line 4037
ERROR:
helix.h::HelicalSegmentPriorInfoEntry::operator<(): A pair of same helical segments is found!
=== Backtrace  ===
/opt/relion/x64/relion-5.0_beta-1/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKNSt7__cxx1112bas>
/opt/relion/x64/relion-5.0_beta-1/bin/relion_refine_mpi(_ZNK28HelicalSegmentPriorInfoEntryltE>
/opt/relion/x64/relion-5.0_beta-1/bin/relion_refine_mpi(+0x263993) [0x5638fcf3f993]
/opt/relion/x64/relion-5.0_beta-1/bin/relion_refine_mpi(+0x264132) [0x5638fcf40132]
/opt/relion/x64/relion-5.0_beta-1/bin/relion_refine_mpi(+0x28f73b) [0x5638fcf6b73b]
/opt/relion/x64/relion-5.0_beta-1/bin/relion_refine_mpi(_Z36updatePriorsForHelicalReconstruct>
/opt/relion/x64/relion-5.0_beta-1/bin/relion_refine_mpi(_ZN14MlOptimiserMpi7iterateEv+0x1651)>
/opt/relion/x64/relion-5.0_beta-1/bin/relion_refine_mpi(main+0x84) [0x5638fcdd57e4]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7fa1dac4ed90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7fa1dac4ee40]
/opt/relion/x64/relion-5.0_beta-1/bin/relion_refine_mpi(_start+0x25) [0x5638fcdd9285]
==================
ERROR:
helix.h::HelicalSegmentPriorInfoEntry::operator<(): A pair of same helical segments is found!
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
==================