RELION 3.1: one of your half sets has no segments

[davidmbelnap]

I used data from an old RELION project. Using the Subset selection function, I wanted to select particles that had a CTF resolution better than 3.5 angs. I ran that function without any problems, but when I used that output as input into Refine3D, I got an error that one of my half sets has no segments. If I use the old, unfiltered data, Refine3D runs fine.

Environment:

• OS: CentOS Linux 7 (Core)
• MPI runtime: Intel MPI 2019.5.281
• RELION version: RELION 3.1-beta (3.1-beta-commit-a6aaa5)
• Memory: two nodes with 128 GB each
• GPU: using CPUs

Dataset:

• Box size: 158 pixels
• Pixel size: 1.39 angs.
• Number of particles: 51,217 in data set (particles.star) where problem occurred; 127,702 total picked particles in larger data set, all boxes are the same size
• Description: small icosahedral virus

Job options:

• Type of job: Refine3D
• Number of MPI processes: 47
• Number of threads: 1
• Full command (see note.txt in the job directory):
  which relion_refine_mpi --o Refine3D/job059/run --auto_refine --split_random_halves --i Select/job058/particles.star --ref Refine3D/job036/run_cl
  ass001.mrc --ini_high 50 --dont_combine_weights_via_disc --no_parallel_disc_io --pool 3 --pad 2 --ctf --ctf_corrected_ref --particle_diameter 210
  --flatten_solvent --oversampling 1 --healpix_order 2 --auto_local_healpix_order 4 --offset_range 5 --offset_step 2 --sym I1 --low_resol_join_halves
  40 --norm --scale --j 1 --pipeline_control Refine3D/job059/

Error message:

in: /uufs/chpc.utah.edu/sys/srcdir/relion/3.1-beta-101519/src/exp_model.cpp, line 362
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
in: /uufs/chpc.utah.edu/sys/srcdir/relion/3.1-beta-101519/src/exp_model.cpp, line 362
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
=== Backtrace  ===
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x48) [0x443d48]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0xd5f) [0x5c773f]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0xe9) [0x4a0ed9]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x46) [0x4a1ce6]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(main+0x75) [0x437925]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2b14b4e8e3d5]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi() [0x4377e9]
==================
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
in: /uufs/chpc.utah.edu/sys/srcdir/relion/3.1-beta-101519/src/exp_model.cpp, line 362
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
in: /uufs/chpc.utah.edu/sys/srcdir/relion/3.1-beta-101519/src/exp_model.cpp, line 362
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
=== Backtrace  ===
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x48) [0x443d48]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0xd5f) [0x5c773f]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0xe9) [0x4a0ed9]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x46) [0x4a1ce6]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(main+0x75) [0x437925]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2ae3911703d5]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi() [0x4377e9]
==================
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
=== Backtrace  ===
in: /uufs/chpc.utah.edu/sys/srcdir/relion/3.1-beta-101519/src/exp_model.cpp, line 362
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
=== Backtrace  ===
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x48) [0x443d48]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0xd5f) [0x5c773f]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0xe9) [0x4a0ed9]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x46) [0x4a1ce6]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(main+0x75) [0x437925]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2b36109223d5]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi() [0x4377e9]
==================
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x48) [0x443d48]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0xd5f) [0x5c773f]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0xe9) [0x4a0ed9]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x46) [0x4a1ce6]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(main+0x75) [0x437925]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2ad992e653d5]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi() [0x4377e9]in: /uufs/chpc.utah.edu/sys/srcdir/relion/3.1-beta-101519/
src/exp_model.cpp, line 362
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
=== Backtrace  ===
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x48) [0x443d48]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0xd5f) [0x5c773f]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0xe9) [0x4a0ed9]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x46) [0x4a1ce6]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(main+0x75) [0x437925]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2aef9d7b33d5]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi() [0x4377e9]
==================
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.

==================
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
in: /uufs/chpc.utah.edu/sys/srcdir/relion/3.1-beta-101519/src/exp_model.cpp, line 362
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
=== Backtrace  ===
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x48) [0x443d48]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0xd5f) [0x5c773f]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0xe9) [0x4a0ed9]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x46) [0x4a1ce6]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(main+0x75) [0x437925]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2b8cb5cd13d5]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi() [0x4377e9]
==================
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
in: /uufs/chpc.utah.edu/sys/srcdir/relion/3.1-beta-101519/src/exp_model.cpp, line 362
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
=== Backtrace  ===
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x48) [0x443d48]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0xd5f) [0x5c773f]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0xe9) [0x4a0ed9]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x46) [0x4a1ce6]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(main+0x75) [0x437925]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2ab3f4fc03d5]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi() [0x4377e9]
==================
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
Abort(1) on node 24 (rank 24 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 24
in: /uufs/chpc.utah.edu/sys/srcdir/relion/3.1-beta-101519/src/exp_model.cpp, line 362
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
=== Backtrace  ===
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x48) [0x443d48]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0xd5f) [0x5c773f]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0xe9) [0x4a0ed9]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x46) [0x4a1ce6]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(main+0x75) [0x437925]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2b63e89443d5]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi() [0x4377e9]
==================
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
in: /uufs/chpc.utah.edu/sys/srcdir/relion/3.1-beta-101519/src/exp_model.cpp, line 362
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
=== Backtrace  ===
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x48) [0x443d48]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0xd5f) [0x5c773f]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0xe9) [0x4a0ed9]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x46) [0x4a1ce6]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(main+0x75) [0x437925]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2b331cec53d5]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi() [0x4377e9]
==================
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
in: /uufs/chpc.utah.edu/sys/srcdir/relion/3.1-beta-101519/src/exp_model.cpp, line 362
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
=== Backtrace  ===
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x48) [0x443d48]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0xd5f) [0x5c773f]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0xe9) [0x4a0ed9]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x46) [0x4a1ce6]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(main+0x75) [0x437925]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2b46576893d5]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi() [0x4377e9]
==================
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
in: /uufs/chpc.utah.edu/sys/srcdir/relion/3.1-beta-101519/src/exp_model.cpp, line 362
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
=== Backtrace  ===
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x48) [0x443d48]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0xd5f) [0x5c773f]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0xe9) [0x4a0ed9]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x46) [0x4a1ce6]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(main+0x75) [0x437925]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2af91bcc03d5]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi() [0x4377e9]
==================
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
in: /uufs/chpc.utah.edu/sys/srcdir/relion/3.1-beta-101519/src/exp_model.cpp, line 362
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
=== Backtrace  ===
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x48) [0x443d48]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0xd5f) [0x5c773f]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0xe9) [0x4a0ed9]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x46) [0x4a1ce6]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(main+0x75) [0x437925]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2af1316bb3d5]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi() [0x4377e9]
==================
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
in: /uufs/chpc.utah.edu/sys/srcdir/relion/3.1-beta-101519/src/exp_model.cpp, line 362
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
=== Backtrace  ===
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x48) [0x443d48]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0xd5f) [0x5c773f]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0xe9) [0x4a0ed9]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x46) [0x4a1ce6]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(main+0x75) [0x437925]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2adcacc573d5]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi() [0x4377e9]
==================
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
in: /uufs/chpc.utah.edu/sys/srcdir/relion/3.1-beta-101519/src/exp_model.cpp, line 362
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
=== Backtrace  ===
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x48) [0x443d48]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0xd5f) [0x5c773f]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0xe9) [0x4a0ed9]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x46) [0x4a1ce6]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(main+0x75) [0x437925]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2abaafea53d5]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi() [0x4377e9]
==================
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
in: /uufs/chpc.utah.edu/sys/srcdir/relion/3.1-beta-101519/src/exp_model.cpp, line 362
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
=== Backtrace  ===
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x48) [0x443d48]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0xd5f) [0x5c773f]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0xe9) [0x4a0ed9]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x46) [0x4a1ce6]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(main+0x75) [0x437925]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2b6a63ba33d5]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi() [0x4377e9]
==================
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
=== Backtrace  ===
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x48) [0x443d48]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0xd5f) [0x5c773f]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0xe9) [0x4a0ed9]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x46) [0x4a1ce6]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(main+0x75) [0x437925]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2b26554193d5]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi() [0x4377e9]
==================
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
in: /uufs/chpc.utah.edu/sys/srcdir/relion/3.1-beta-101519/src/exp_model.cpp, line 362
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
=== Backtrace  ===
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x48) [0x443d48]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0xd5f) [0x5c773f]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0xe9) [0x4a0ed9]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x46) [0x4a1ce6]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(main+0x75) [0x437925]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2b50bb4103d5]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi() [0x4377e9]
==================
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
in: /uufs/chpc.utah.edu/sys/srcdir/relion/3.1-beta-101519/src/exp_model.cpp, line 362
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
=== Backtrace  ===
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x48) [0x443d48]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0xd5f) [0x5c773f]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0xe9) [0x4a0ed9]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x46) [0x4a1ce6]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(main+0x75) [0x437925]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2b540ea593d5]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi() [0x4377e9]
==================
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
in: /uufs/chpc.utah.edu/sys/srcdir/relion/3.1-beta-101519/src/exp_model.cpp, line 362
ERROR: 
ERROR: one of your half sets has no segments. Is rlnRandomSubset set to 1 or 2 in your particles STAR file? Or in case you're doing helical, half-s
ets are always per-filament, so provide at least 2 filaments.
Abort(1) on node 15 (rank 15 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 15
=== Backtrace  ===

[biochem-fan]

As the message suggests, did you make sure the input STAR file contains the rlnRandomSubset column and it has both and only 1 and 2?

[davidmbelnap]

The particles.star that does work does not contain a rlnRandomSubset column either. Here is what it contains: # RELION; version 3.0-beta-2 data_ loop_ _rlnCoordinateX #1 _rlnCoordinateY #2 _rlnClassNumber #3 _rlnAutopickFigureOfMerit #4 _rlnAnglePsi #5 _rlnImageName #6 _rlnMicrographName #7 _rlnMagnification #8 _rlnDetectorPixelSize #9 _rlnCtfMaxResolution #10 _rlnCtfFigureOfMerit #11 _rlnVoltage #12 _rlnDefocusU #13 _rlnDefocusV #14 _rlnDefocusAngle #15 _rlnSphericalAberration #16 _rlnCtfBfactor #17 _rlnCtfScalefactor #18 _rlnPhaseShift #19 _rlnAmplitudeContrast #20 _rlnGroupNumber #21 _rlnAngleRot #22 _rlnAngleTilt #23 _rlnOriginX #24 _rlnOriginY #25 _rlnNormCorrection #26 _rlnLogLikeliContribution #27 _rlnMaxValueProbDistribution #28 _rlnNrOfSignificantSamples #29 After sorting (Subset selection) on values of rlnCtfMaxResolution between 0.0 and 3.5 in the above particles.star file, this is the header for the resulting particles.star file. I edited rlnOpticsGroupName from “opticsGroup0” to “opticsGroup1”. That had no effect on running Refine3D: # version 30001 data_optics loop_ _rlnOpticsGroup #1 _rlnOpticsGroupName #2 _rlnAmplitudeContrast #3 _rlnSphericalAberration #4 _rlnVoltage #5 _rlnImagePixelSize #6 _rlnMicrographOriginalPixelSize #7 _rlnImageSize #8 _rlnImageDimensionality #9 1 opticsGroup1 0.100000 2.700000 300.000000 1.389992 1.389992 158 2 # version 30001 data_ loop_ _rlnCoordinateX #1 _rlnCoordinateY #2 _rlnClassNumber #3 _rlnAutopickFigureOfMerit #4 _rlnAnglePsi #5 _rlnImageName #6 _rlnMicrographName #7 _rlnCtfMaxResolution #8 _rlnCtfFigureOfMerit #9 _rlnDefocusU #10 _rlnDefocusV #11 _rlnDefocusAngle #12 _rlnCtfBfactor #13 _rlnCtfScalefactor #14 _rlnPhaseShift #15 _rlnGroupNumber #16 _rlnAngleRot #17 _rlnAngleTilt #18 _rlnNormCorrection #19 _rlnLogLikeliContribution #20 _rlnMaxValueProbDistribution #21 _rlnNrOfSignificantSamples #22 _rlnOpticsGroup #23 _rlnOriginXAngst #24 _rlnOriginYAngst #25 On Oct 20, 2019, at 12:44 AM, biochem_fan <notifications@github.com<mailto:notifications@github.com>> wrote: As the message suggests, did you make sure the input STAR file contains the rlnRandomSubset column and it has both and only 1 and 2? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#521?email_source=notifications&email_token=ANQUDY5HFOEGXFMLXYEBJX3QPP43NA5CNFSM4JCSGRX2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEBYDUQA#issuecomment-544225856>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ANQUDY6LB66AOIMW2263MPDQPP43NANCNFSM4JCSGRXQ>.

[biochem-fan]

OK, this seems to be a bug in Subset Selection.
Meanwhile, could you please change data_ to data_particles?

data_

loop_
_rlnCoordinateX #1
_rlnCoordinateY #2
_rlnClassNumber #3

[biochem-fan]

In star_handler.cpp, read_check_ignore_optics() should assign a correct table name.

[biochem-fan]

I hopefully fixed this by the commit above. Please try subset selection again.

[biochem-fan]

No response for 3 weeks. Closing this.

[davidmbelnap]

My apologies for not responding until now, but I didn't know a new version of the RELION was available until this week. I have asked my computing center to install it. I can report if the bug has been fixed after the new version is installed.

In the meantime, changing "data_" to "data_particles" prevented the error from occurring.