Csparc2star.py - rlnImageName or rlnReferenceImage error in Relion3.1-beta

Environment

  • cryoSPARC version: v2.15.0
  • CUDA version: v10.0.130
  • OS: CentOS 7
  • Relion version: 3.1-beta-commit-f2335a

Issue

  • Type of Issue
    Export of particles from cryoSPARC to Relion 3.1-beta using csparc2star.py script.
  • Explain the problem in as much detail as possible
    After running a 2D classification job on cryoSPARC, I am trying to export the particles to Relion for Autopicking. The csparc2star.py command is (added --lowlevel debug for detail):
csparc2star.py P1_J62_passthrough_particles_selected.cs particles_selected.cs particles_selected_t3.star --boxsize 512 --copy-micrograph-coordinates /data/work/elliot/processing/A2326_5/Extract/job373/particles.star --loglevel debug
    Detected CryoSPARC 2+ .cs file
    Reading primary file
    Converting normalized particle coordinates to absolute
    Converted particle coordinates from normalized to absolute
    Classification parameters not found
    Reading auxiliary file particles_selected.cs
    Trying to merge: blob/path, blob/idx, blob/shape, blob/psize_A, blob/sign, alignments2D/split, alignments2D/shift, alignments2D/pose, alignments2D/psize_A, alignments2D/error, alignments2D/error_min, alignments2D/resid_pow, alignments2D/slice_pow, alignments2D/image_pow, alignments2D/cross_cor, alignments2D/alpha, alignments2D/alpha_min, alignments2D/weight, alignments2D/pose_ess, alignments2D/shift_ess, alignments2D/class_posterior, alignments2D/class, alignments2D/class_ess
    Merging: rlnDetectorPixelSize, ucsfImagePath, ucsfImageIndex
    Directly copied fields: rlnOpticsGroup, rlnAmplitudeContrast, rlnDefocusAngle, rlnPhaseShift, rlnVoltage, rlnDefocusV, rlnSphericalAberration, rlnMicrographName, rlnCtfBfactor, ucsfUid, rlnDefocusU, rlnCoordinateX, rlnCoordinateY, rlnDetectorPixelSize, ucsfImagePath, ucsfImageIndex, rlnMagnification
    Converting DEFOCUSANGLE from degrees to radians
    Converting PHASESHIFT from degrees to radians
    Angular alignment parameters not found
    /usr/local/pyem/pyem/star.py:531: FutureWarning: Columnar iteration over characters will be deprecated in future releases.
      df[UCSF.IMAGE_INDEX], df[UCSF.IMAGE_PATH] = \
    /usr/local/pyem/pyem/star.py:539: FutureWarning: Columnar iteration over characters will be deprecated in future releases.
      df[UCSF.IMAGE_ORIGINAL_INDEX], df[UCSF.IMAGE_ORIGINAL_PATH] = \
    Coordinates merge key: ['ucsfImageBasename', 'ucsfImageIndex']
    Output fields: rlnOpticsGroup, rlnAmplitudeContrast, rlnDefocusAngle, rlnPhaseShift, rlnVoltage, rlnDefocusV, rlnSphericalAberration, rlnMicrographName, rlnCtfBfactor, rlnDefocusU, rlnCoordinateX, rlnCoordinateY, rlnImageName, rlnImagePixelSize, rlnImageDimensionality

As was mentioned in a previous thread, I manually added the _rlnImageSize field in the output .star file data_optics header and imported it into Relion. The resulting .star file shows:

I am trying to use those particles as references for Autopicking in Relion, but I get a rlnReferenceImage or rlnImageName error message (see below). I tried re-extracting the particles without re-centering and get an error about reading the header for the mrcs particles stack.
To note: I have also tried running an relion_convert_star command and the output .star file is empty.

  • Error message/traceback

Autopick error

=== Backtrace  ===
/usr/local/relion-3.1b/bin/relion_autopick_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x438dc1]
/usr/local/relion-3.1b/bin/relion_autopick_mpi(_ZN10AutoPicker10initialiseEv+0x25e6) [0x44a036]
/usr/local/relion-3.1b/bin/relion_autopick_mpi(main+0x3e) [0x432ede]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x7feae45d5495]
/usr/local/relion-3.1b/bin/relion_autopick_mpi() [0x4368bf]
==================
ERROR: 
AutoPicker::initialise ERROR: either provide rlnReferenceImage or rlnImageName in the reference STAR file!
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
:
system msg for write_line failure : Bad file descriptor

Extract error

ERROR: 
rwMRC: error in reading header of image Extract/job428/Micrographs/FoilHole_20594641_Data_20595273_20595274_20191120_0028_Fractions.mrcs
in: /usr/local/relion_3.1beta_source/src/rwMRC.h, line 157
ERROR: 
rwMRC: error in reading header of image Extract/job428/Micrographs/FoilHole_20594641_Data_20595273_20595274_20191120_0028_Fractions.mrcs
=== Backtrace  ===
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x420da1]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(_ZN5ImageIdE7readMRCElbRK8FileName+0xe3b) [0x43c41b]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(_ZN5ImageIdE5_readERK8FileNameR13fImageHandlerblbb+0x173) [0x43e593]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(_ZN5ImageIdE4readERK8FileNameblbb+0xf7) [0x43ed97]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(_ZN5ImageIdE6_writeERK8FileNameR13fImageHandlerlbi+0xa21) [0x43fb71]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(_ZN13Preprocessing25performPerImageOperationsER5ImageIdE8FileNamellddRdS4_S4_S4_+0xac7) [0x42b157]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(_ZN13Preprocessing33extractParticlesFromOneMicrographER13MetaDataTable8FileNameiS2_S2_RllRdS4_S4_S4_+0xe9c) [0x42c8cc]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(_ZN13Preprocessing31extractParticlesFromFieldOfViewE8FileNamel+0x5c3) [0x431583]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi19runExtractParticlesEv+0x446) [0x4208d6]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi3runEv+0x12) [0x420c92]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(main+0x3b) [0x41dbcb]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x7fa0c7a82495]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi() [0x41e4ff]
==================
ERROR: 
rwMRC: error in reading header of image Extract/job428/Micrographs/FoilHole_20594641_Data_20595273_20595274_20191120_0028_Fractions.mrcs
=== Backtrace  ===
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
:
system msg for write_line failure : Bad file descriptor
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x420da1]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(_ZN5ImageIdE7readMRCElbRK8FileName+0xe3b) [0x43c41b]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(_ZN5ImageIdE5_readERK8FileNameR13fImageHandlerblbb+0x173) [0x43e593]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(_ZN5ImageIdE4readERK8FileNameblbb+0xf7) [0x43ed97]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(_ZN5ImageIdE6_writeERK8FileNameR13fImageHandlerlbi+0xa21) [0x43fb71]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(_ZN13Preprocessing25performPerImageOperationsER5ImageIdE8FileNamellddRdS4_S4_S4_+0xac7) [0x42b157]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(_ZN13Preprocessing33extractParticlesFromOneMicrographER13MetaDataTable8FileNameiS2_S2_RllRdS4_S4_S4_+0xe9c) [0x42c8cc]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(_ZN13Preprocessing31extractParticlesFromFieldOfViewE8FileNamel+0x5c3) [0x431583]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi19runExtractParticlesEv+0x446) [0x4208d6]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi3runEv+0x12) [0x420c92]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi(main+0x3b) [0x41dbcb]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x7f64d021b495]
/usr/local/relion-3.1b/bin/relion_preprocess_mpi() [0x41e4ff]
==================
ERROR: 
rwMRC: error in reading header of image Extract/job428/Micrographs/FoilHole_20594641_Data_20595273_20595274_20191120_0028_Fractions.mrcs
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
:
system msg for write_line failure : Bad file descriptor

What might be going wrong here?
Thanks in advance for any insight! Please let me know if any additional information is needed.
Best,
EJC