hi there,
I tried to convert selected particles from a 2D classification job to .star file:
csparc2star.py particles_selected.cs P54_J6_passthrough_particles_selected.cs P54_J6_particles.star
and/or
csparc2star.py --logelevel debug particles_selected.cs P54_J6_passthrough_particles_selected.cs P54_J6_particles_selected2.star
however when I run 3D refine in Relion I get this error:
in: /packages/RELION/relion-3.1.2/src/exp_model.cpp, line 344
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-sets are always per-filament, so provide at least 2 filaments.
=== Backtrace ===
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x67) [0x562b6e2d9c67]
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0x1142) [0x562b6e37de92]
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x261) [0x562b6e2f9b91]
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x9d2) [0x562b6e2fbb92]
/opt/relion/3.1.2/bin/relion_refine_mpi(main+0x4a) [0x562b6e2c490a]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xeb) [0x7f25f4dc709b]
/opt/relion/3.1.2/bin/relion_refine_mpi(_start+0x2a) [0x562b6e2c7c5a]
==================
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-sets are always per-filament, so provide at least 2 filaments.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
in: /packages/RELION/relion-3.1.2/src/exp_model.cpp, line 344
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-sets are always per-filament, so provide at least 2 filaments.
=== Backtrace ===
in: /packages/RELION/relion-3.1.2/src/exp_model.cpp, line 344
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-sets are always per-filament, so provide at least 2 filaments.
=== Backtrace ===
in: /packages/RELION/relion-3.1.2/src/exp_model.cpp, line 344
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-sets are always per-filament, so provide at least 2 filaments.
=== Backtrace ===
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x67) [0x55a5d97a3c67]
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0x1142) [0x55a5d9847e92]
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x261) [0x55a5d97c3b91]
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x9d2) [0x55a5d97c5b92]
/opt/relion/3.1.2/bin/relion_refine_mpi(main+0x4a) [0x55a5d978e90a]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xeb) [0x7f29aebb009b]
/opt/relion/3.1.2/bin/relion_refine_mpi(_start+0x2a) [0x55a5d9791c5a]
==================
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-sets are always per-filament, so provide at least 2 filaments.
in: /packages/RELION/relion-3.1.2/src/exp_model.cpp, line 344
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-sets are always per-filament, so provide at least 2 filaments.
=== Backtrace ===
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x67) [0x55f313b35c67]
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0x1142) [0x55f313bd9e92]
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x261) [0x55f313b55b91]
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x9d2) [0x55f313b57b92]
/opt/relion/3.1.2/bin/relion_refine_mpi(main+0x4a) [0x55f313b2090a]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xeb) [0x7f5967be909b]
/opt/relion/3.1.2/bin/relion_refine_mpi(_start+0x2a) [0x55f313b23c5a]
==================
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-sets are always per-filament, so provide at least 2 filaments.
in: /packages/RELION/relion-3.1.2/src/exp_model.cpp, line 344
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-sets are always per-filament, so provide at least 2 filaments.
=== Backtrace ===
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x67) [0x55b5403ddc67]
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0x1142) [0x55b540481e92]
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x261) [0x55b5403fdb91]
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x9d2) [0x55b5403ffb92]
/opt/relion/3.1.2/bin/relion_refine_mpi(main+0x4a) [0x55b5403c890a]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xeb) [0x7fe681ebd09b]
/opt/relion/3.1.2/bin/relion_refine_mpi(_start+0x2a) [0x55b5403cbc5a]
==================
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-sets are always per-filament, so provide at least 2 filaments.
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x67) [0x5601b51b2c67]
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0x1142) [0x5601b5256e92]
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x261) [0x5601b51d2b91]
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x9d2) [0x5601b51d4b92]
/opt/relion/3.1.2/bin/relion_refine_mpi(main+0x4a) [0x5601b519d90a]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xeb) [0x7f61cc5bc09b]
/opt/relion/3.1.2/bin/relion_refine_mpi(_start+0x2a) [0x5601b51a0c5a]
==================
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-sets are always per-filament, so provide at least 2 filaments.
in: /packages/RELION/relion-3.1.2/src/exp_model.cpp, line 344
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-sets are always per-filament, so provide at least 2 filaments.
=== Backtrace ===
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x67) [0x55f93d874c67]
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0x1142) [0x55f93d918e92]
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x261) [0x55f93d894b91]
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x9d2) [0x55f93d896b92]
/opt/relion/3.1.2/bin/relion_refine_mpi(main+0x4a) [0x55f93d85f90a]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xeb) [0x7f88a4c3f09b]
/opt/relion/3.1.2/bin/relion_refine_mpi(_start+0x2a) [0x55f93d862c5a]
==================
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-sets are always per-filament, so provide at least 2 filaments.
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x67) [0x5627f4b11c67]
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN10Experiment29divideParticlesInRandomHalvesEib+0x1142) [0x5627f4bb5e92]
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x261) [0x5627f4b31b91]
/opt/relion/3.1.2/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x9d2) [0x5627f4b33b92]
/opt/relion/3.1.2/bin/relion_refine_mpi(main+0x4a) [0x5627f4afc90a]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xeb) [0x7f91e892e09b]
/opt/relion/3.1.2/bin/relion_refine_mpi(_start+0x2a) [0x5627f4affc5a]
==================
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-sets are always per-filament, so provide at least 2 filaments.
[89679] 6 more processes have sent help message help-mpi-api.txt / mpi-abort
[89679] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
Am I doing something wrong with the conversion csparc2star.py?
thanks in advance for your feedback.