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Subject:

Re: relion_convert_star output not accepted by Extraction job (Relion 3.1 beta)

From:

Oliver Clarke <[log in to unmask]>

Reply-To:

Oliver Clarke <[log in to unmask]>

Date:

Sun, 20 Oct 2019 16:07:34 -0400

Content-Type:

multipart/mixed

Parts/Attachments:
Parts/Attachments

text/plain (12 lines) , particles_before.txt (33 lines) , error.txt (206 lines) , mics_before.txt (17 lines) , Unknown Name (40 lines) 

Thanks Takanori - here are samples of the files before conversion, and the full error message.

Cheers
Oli


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data_images

loop_
_rlnImageName #1
_rlnMicrographName #2
_rlnCoordinateX #3
_rlnCoordinateY #4
_rlnAngleRot #5
_rlnAngleTilt #6
_rlnAnglePsi #7
_rlnOriginX #8
_rlnOriginY #9
_rlnVoltage #10
_rlnMagnification #11
_rlnDetectorPixelSize #12
_rlnDefocusU #13
_rlnDefocusV #14
_rlnDefocusAngle #15
_rlnSphericalAberration #16
_rlnPhaseShift #17
_rlnAmplitudeContrast #18
_rlnClassNumber #19
_rlnRandomSubset #20
[log in to unmask] csparc_mics/19oct14b_test_00004Gr_00015Sq_v01_00002Hln_00002Enn.frames_patch_aligned_doseweighted.mrc 2493 4530 -59.438374 103.514633 -120.361206 5.718750 -8.718750 300.000000 10000.000000 0.827500 2899.840332 2819.877930 -28.248791 2.700000 0.000000 0.100000 1 1
[log in to unmask] csparc_mics/19oct14b_test_00004Gr_00015Sq_v01_00002Hln_00002Enn.frames_patch_aligned_doseweighted.mrc 3584 765 21.344009 83.019714 55.912521 -7.781250 -9.843750 300.000000 10000.000000 0.827500 3689.104980 3609.142578 -28.248791 2.700000 0.000000 0.100000 1 1
[log in to unmask] csparc_mics/19oct14b_test_00004Gr_00015Sq_v01_00002Hln_00002Enn.frames_patch_aligned_doseweighted.mrc 1561 3255 114.085648 99.632111 152.295746 -3.656250 -12.093750 300.000000 10000.000000 0.827500 2927.461426 2847.499023 -28.248791 2.700000 0.000000 0.100000 1 1
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in: /home/user/software/relion/src/jaz/obs_model.cpp, line 178
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
=== Backtrace  ===
in: /home/user/software/relion/src/jaz/obs_model.cpp, line 178
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
=== Backtrace  ===
in: /home/user/software/relion/src/jaz/obs_model.cpp, line 178
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
=== Backtrace  ===
in: /home/user/software/relion/src/jaz/obs_model.cpp, line 178
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
=== Backtrace  ===
in: /home/user/software/relion/src/jaz/obs_model.cpp, line 178
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
=== Backtrace  ===
/usr/local/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x77) [0x5624096f10b7]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModelC1ERK13MetaDataTableb+0x134a) [0x56240973409a]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModel10loadSafelyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS_R13MetaDataTableS5_ib+0x4b9) [0x562409734d49]
/usr/local/bin/relion_preprocess_mpi(_ZN13Preprocessing10initialiseEv+0x124) [0x562409713df4]
/usr/local/bin/relion_preprocess_mpi(main+0x47) [0x5624096e4df7]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f3c55570b97]
/usr/local/bin/relion_preprocess_mpi(_start+0x2a) [0x5624096e57aa]
==================
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
/usr/local/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x77) [0x55e4cb3bf0b7]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModelC1ERK13MetaDataTableb+0x134a) [0x55e4cb40209a]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModel10loadSafelyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS_R13MetaDataTableS5_ib+0x4b9) [0x55e4cb402d49]
/usr/local/bin/relion_preprocess_mpi(_ZN13Preprocessing10initialiseEv+0x124) [0x55e4cb3e1df4]
/usr/local/bin/relion_preprocess_mpi(main+0x47) [0x55e4cb3b2df7]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f4ff6894b97]
/usr/local/bin/relion_preprocess_mpi(_start+0x2a) [0x55e4cb3b37aa]
==================
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
/usr/local/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x77) [0x55f53e8060b7]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModelC1ERK13MetaDataTableb+0x134a) [0x55f53e84909a]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModel10loadSafelyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS_R13MetaDataTableS5_ib+0x4b9) [0x55f53e849d49]
/usr/local/bin/relion_preprocess_mpi(_ZN13Preprocessing10initialiseEv+0x124) [0x55f53e828df4]
/usr/local/bin/relion_preprocess_mpi(main+0x47) [0x55f53e7f9df7]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f075fe0db97]
/usr/local/bin/relion_preprocess_mpi(_start+0x2a) [0x55f53e7fa7aa]
==================
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
/usr/local/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x77) [0x559a755190b7]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModelC1ERK13MetaDataTableb+0x134a) [0x559a7555c09a]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModel10loadSafelyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS_R13MetaDataTableS5_ib+0x4b9) [0x559a7555cd49]
/usr/local/bin/relion_preprocess_mpi(_ZN13Preprocessing10initialiseEv+0x124) [0x559a7553bdf4]
/usr/local/bin/relion_preprocess_mpi(main+0x47) [0x559a7550cdf7]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f8e46da9b97]
/usr/local/bin/relion_preprocess_mpi(_start+0x2a) [0x559a7550d7aa]
==================
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
in: /home/user/software/relion/src/jaz/obs_model.cpp, line 178
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
=== Backtrace  ===
/usr/local/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x77) [0x55dc4b32c0b7]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModelC1ERK13MetaDataTableb+0x134a) [0x55dc4b36f09a]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModel10loadSafelyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS_R13MetaDataTableS5_ib+0x4b9) [0x55dc4b36fd49]
/usr/local/bin/relion_preprocess_mpi(_ZN13Preprocessing10initialiseEv+0x124) [0x55dc4b34edf4]
/usr/local/bin/relion_preprocess_mpi(main+0x47) [0x55dc4b31fdf7]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7ff6c1f2eb97]
/usr/local/bin/relion_preprocess_mpi(_start+0x2a) [0x55dc4b3207aa]
==================
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
in: /home/user/software/relion/src/jaz/obs_model.cpp, line 178
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
=== Backtrace  ===
/usr/local/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x77) [0x56053baba0b7]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModelC1ERK13MetaDataTableb+0x134a) [0x56053bafd09a]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModel10loadSafelyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS_R13MetaDataTableS5_ib+0x4b9) [0x56053bafdd49]
/usr/local/bin/relion_preprocess_mpi(_ZN13Preprocessing10initialiseEv+0x124) [0x56053badcdf4]
/usr/local/bin/relion_preprocess_mpi(main+0x47) [0x56053baaddf7]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f3290fddb97]
/usr/local/bin/relion_preprocess_mpi(_start+0x2a) [0x56053baae7aa]
==================
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
/usr/local/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x77) [0x55b4485250b7]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModelC1ERK13MetaDataTableb+0x134a) [0x55b44856809a]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModel10loadSafelyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS_R13MetaDataTableS5_ib+0x4b9) [0x55b448568d49]
/usr/local/bin/relion_preprocess_mpi(_ZN13Preprocessing10initialiseEv+0x124) [0x55b448547df4]
/usr/local/bin/relion_preprocess_mpi(main+0x47) [0x55b448518df7]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7fe67f51bb97]
/usr/local/bin/relion_preprocess_mpi(_start+0x2a) [0x55b4485197aa]
==================
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
in: /home/user/software/relion/src/jaz/obs_model.cpp, line 178
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
=== Backtrace  ===
/usr/local/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x77) [0x55ad57b260b7]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModelC1ERK13MetaDataTableb+0x134a) [0x55ad57b6909a]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModel10loadSafelyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS_R13MetaDataTableS5_ib+0x4b9) [0x55ad57b69d49]
/usr/local/bin/relion_preprocess_mpi(_ZN13Preprocessing10initialiseEv+0x124) [0x55ad57b48df4]
/usr/local/bin/relion_preprocess_mpi(main+0x47) [0x55ad57b19df7]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f27d98d4b97]
/usr/local/bin/relion_preprocess_mpi(_start+0x2a) [0x55ad57b1a7aa]
==================
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
in: /home/user/software/relion/src/jaz/obs_model.cpp, line 178
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
=== Backtrace  ===
/usr/local/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x77) [0x55adb85060b7]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModelC1ERK13MetaDataTableb+0x134a) [0x55adb854909a]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModel10loadSafelyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS_R13MetaDataTableS5_ib+0x4b9) [0x55adb8549d49]in: /home/user/software/relion/src/jaz/obs_model.cpp, line 178
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
=== Backtrace  ===
/usr/local/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x77) [0x55afe22370b7]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModelC1ERK13MetaDataTableb+0x134a) [0x55afe227a09a]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModel10loadSafelyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS_R13MetaDataTableS5_ib+0x4b9) [0x55afe227ad49]
/usr/local/bin/relion_preprocess_mpi(_ZN13Preprocessing10initialiseEv+0x124) [0x55afe2259df4]
/usr/local/bin/relion_preprocess_mpi(main+0x47) [0x55afe222adf7]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f6b1fdf4b97]
/usr/local/bin/relion_preprocess_mpi(_start+0x2a) [0x55afe222b7aa]
==================
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
in: /home/user/software/relion/src/jaz/obs_model.cpp, line 178
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
=== Backtrace  ===
/usr/local/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x77) [0x55ea50c0f0b7]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModelC1ERK13MetaDataTableb+0x134a) [0x55ea50c5209a]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModel10loadSafelyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS_R13MetaDataTableS5_ib+0x4b9) [0x55ea50c52d49]
/usr/local/bin/relion_preprocess_mpi(_ZN13Preprocessing10initialiseEv+0x124) [0x55ea50c31df4]
/usr/local/bin/relion_preprocess_mpi(main+0x47) [0x55ea50c02df7]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f993c9dfb97]
/usr/local/bin/relion_preprocess_mpi(_start+0x2a) [0x55ea50c037aa]
==================
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
in: /home/user/software/relion/src/jaz/obs_model.cpp, line 178
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
=== Backtrace  ===
/usr/local/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x77) [0x555c220bd0b7]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModelC1ERK13MetaDataTableb+0x134a) [0x555c2210009a]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModel10loadSafelyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS_R13MetaDataTableS5_ib+0x4b9) [0x555c22100d49]
/usr/local/bin/relion_preprocess_mpi(_ZN13Preprocessing10initialiseEv+0x124) [0x555c220dfdf4]
/usr/local/bin/relion_preprocess_mpi(main+0x47) [0x555c220b0df7]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7fb3ca7ebb97]
/usr/local/bin/relion_preprocess_mpi(_start+0x2a) [0x555c220b17aa]
==================
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
in: /home/user/software/relion/src/jaz/obs_model.cpp, line 178
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
=== Backtrace  ===
/usr/local/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x77) [0x56497786a0b7]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModelC1ERK13MetaDataTableb+0x134a) [0x5649778ad09a]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModel10loadSafelyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS_R13MetaDataTableS5_ib+0x4b9) [0x5649778add49]
/usr/local/bin/relion_preprocess_mpi(_ZN13Preprocessing10initialiseEv+0x124) [0x56497788cdf4]
/usr/local/bin/relion_preprocess_mpi(main+0x47) [0x56497785ddf7]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f3f15f7eb97]
/usr/local/bin/relion_preprocess_mpi(_start+0x2a) [0x56497785e7aa]
==================
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
in: /home/user/software/relion/src/jaz/obs_model.cpp, line 178
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
=== Backtrace  ===
/usr/local/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x77) [0x557e43cb20b7]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModelC1ERK13MetaDataTableb+0x134a) [0x557e43cf509a]
/usr/local/bin/relion_preprocess_mpi(_ZN16ObservationModel10loadSafelyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS_R13MetaDataTableS5_ib+0x4b9) [0x557e43cf5d49]
/usr/local/bin/relion_preprocess_mpi(_ZN13Preprocessing10initialiseEv+0x124) [0x557e43cd4df4]
/usr/local/bin/relion_preprocess_mpi(main+0x47) [0x557e43ca5df7]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f6982439b97]
/usr/local/bin/relion_preprocess_mpi(_start+0x2a) [0x557e43ca67aa]
==================
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.

/usr/local/bin/relion_preprocess_mpi(_ZN13Preprocessing10initialiseEv+0x124) [0x55adb8528df4]
/usr/local/bin/relion_preprocess_mpi(main+0x47) [0x55adb84f9df7]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7fa671542b97]
/usr/local/bin/relion_preprocess_mpi(_start+0x2a) [0x55adb84fa7aa]
==================
ERROR: 
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
[ubuntu:14128] 23 more processes have sent help message help-mpi-btl-base.txt / btl:no-nics
[ubuntu:14128] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
[ubuntu:14128] 13 more processes have sent help message help-mpi-api.txt / mpi-abort

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data_images

loop_
_rlnMicrographName #1
csparc_mics/19oct14b_test_00004Gr_00015Sq_v01_00002Hln_00002Enn.frames_patch_aligned_doseweighted.mrc
csparc_mics/19oct14b_test_00004Gr_00015Sq_v01_00003Hln_00002Enn.frames_patch_aligned_doseweighted.mrc
csparc_mics/19oct14b_test_00004Gr_00015Sq_v01_00003Hln_00005Enn.frames_patch_aligned_doseweighted.mrc
csparc_mics/19oct14b_test_00004Gr_00015Sq_v01_00003Hln_00006Enn.frames_patch_aligned_doseweighted.mrc
csparc_mics/19oct14b_test_00004Gr_00015Sq_v01_00003Hln_00007Enn.frames_patch_aligned_doseweighted.mrc
csparc_mics/19oct14b_test_00004Gr_00015Sq_v01_00003Hln_00008Enn.frames_patch_aligned_doseweighted.mrc
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> On Oct 20, 2019, at 3:11 PM, Takanori Nakane <[log in to unmask]> wrote:
> 
> Hi,
> 
> > it is missing required parameters
> 
> Please write the full error message with printed backtrace.
> 
> Please also share the files before conversion as well.
> (Header and just few particles/micrographs are enough)
> 
> Best regards,
> 
> Takanori Nakane
> 
> On 2019/10/20 16:18, Oliver Clarke wrote:
>> Hi,
>> I am trying to convert a star file (converted from cryosparc to relion using csparc2star.py from pyem) for re-extraction of recentered particles. relion_reconstruct has no problems with the file, but when I attempt to re-extract recentered particles, Relion complains that it is missing required parameters in the optics.star (but does not specify what these are). The conversion command I used was:
>> relion_convert_star --i P9_J215.star --o P9_J215_new.star --Cs 2.7 --Q0 0.1
>> I used the same command for both the micrograph and particle star files, and I’ve attached the beginning of both files for debugging.
>> I notice that relion_convert_star does not create an optics group column in the data_particles table of the star file. Should it do so?
>> Cheers
>> Oli
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