Errors when OpticsGroup of corrected_micrographs.star not the same as particles.star

[builab]

Describe your problem

When the corrected_micrographs.star does not have the same OpticsGroup as particles.star for re-extraction, the error happens at the end when joining star files. In this case, it is due to the use of cryosparc conversion. However, there are many cases where we divided OpticsGroups only at the end.

Relion should just overwrite the opticGroups from micrographs.star using particles.star

Environment:

• OS: Ubuntu
• RELION 5.0-beta-0-commit-832d07
• Memory: 512GB

Job options:

• Type of job: Extract particles
• Full command (see note.txt in the job directory):

which relion_preprocess_mpi --i MovieExport/corrected_micrographs.star --reextract_data_star Star/j698_export_noinverty_short.star --part_star Extract/job003/particles.star --pick_star Extract/job003/extractpick.star --part_dir Extract/job003/ --extract --extract_size 512 --float16 --scale 128 --norm --bg_radius 48 --white_dust -1 --black_dust -1 --invert_contrast --pipeline_control Extract/job003/

**Error message:**

Please cite the *full* error message as the example below.


Error message

• Re-extracting particles based on coordinates from input _data.star file
• Star/j698_export_noinverty_short.star
  Extracting particles from the micrographs ...
  50/ 50 sec ............................................................~~(,_,">

Joining metadata of all particles from 20050 micrographs in one STAR file...
The pixel size of the extracted particles in optics group 1 is 5.48 Angstrom/pixel.

RELION version: 5.0-beta-0-commit-832d07
exiting with an error ...

/data2/apps/relion/5.0/bin/relion_preprocess_mpi(_ZN11RelionErrorC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x69) [0x4f6059]
/data2/apps/relion/5.0/bin/relion_preprocess_mpi() [0x44b858]
/data2/apps/relion/5.0/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi3runEv+0x15) [0x537085]
/data2/apps/relion/5.0/bin/relion_preprocess_mpi(main+0x3e) [0x4e809e]
/lib64/libc.so.6(+0x3feb0) [0x7fc00943feb0]
/lib64/libc.so.6(__libc_start_main+0x80) [0x7fc00943ff60]
/data2/apps/relion/5.0/bin/relion_preprocess_mpi(_start+0x25) [0x4eb995]

ERROR:
ERROR: optics group "opticsGroup2" does not exist in micrograph STAR file...

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.