WARNING: You did not specify --angpix_ref. The pixel size in the image header of Refine3D/job019/run_half1_class001_unfil.mrc, 0.824 A/px, is used. WARNING: You did not specify --angpix_ref. The pixel size in the image header of Refine3D/job019/run_half1_class001_unfil.mrc, 0.824 A/px, is used. WARNING: You did not specify --angpix_ref. The pixel size in the image header of Refine3D/job019/run_half1_class001_unfil.mrc, 0.824 A/px, is used. WARNING: You did not specify --angpix_ref. The pixel size in the image header of Refine3D/job019/run_half1_class001_unfil.mrc, 0.824 A/px, is used. WARNING: You did not specify --angpix_ref. The pixel size in the image header of Refine3D/job019/run_half1_class001_unfil.mrc, 0.824 A/px, is used. WARNING: You did not specify --angpix_ref. The pixel size in the image header of Refine3D/job019/run_half1_class001_unfil.mrc, 0.824 A/px, is used. in: /public/EM/RELION/relion-4.0-dev/src/image.h, line 276 ERROR: Cannot read file ../gain-reference.mrc It does not exist in: /public/EM/RELION/relion-4.0-dev/src/image.h, line 276 ERROR: Cannot read file ../gain-reference.mrc It does not exist in: /public/EM/RELION/relion-4.0-dev/src/image.h, line 276 ERROR: Cannot read file ../gain-reference.mrc It does not exist - Warning: unable to load raw movie frames for MotionCorr/job003/Tiff/EER/GridSquare_11092862/Data/FoilHole_11096311_Data_11093776_11093778_20210911_104021_EER.mrc. Possible reasons include lack of the metadata STAR file, the gain reference and/or the movie. - Warning: unable to load raw movie frames for MotionCorr/job003/Tiff/EER/GridSquare_11092862/Data/FoilHole_11096601_Data_11093767_11093769_20210911_110816_EER.mrc. Possible reasons include lack of the metadata STAR file, the gain reference and/or the movie. - Warning: unable to load raw movie frames for MotionCorr/job003/Tiff/EER/GridSquare_11092862/Data/FoilHole_11096454_Data_11093770_11093772_20210911_104258_EER.mrc. Possible reasons include lack of the metadata STAR file, the gain reference and/or the movie. in: /public/EM/RELION/relion-4.0-dev/src/image.h, line 276 ERROR: Cannot read file ../gain-reference.mrc It does not exist - Warning: unable to load raw movie frames for MotionCorr/job003/Tiff/EER/GridSquare_11092862/Data/FoilHole_11096520_Data_11093776_11093778_20210911_104519_EER.mrc. Possible reasons include lack of the metadata STAR file, the gain reference and/or the movie. in: /public/EM/RELION/relion-4.0-dev/src/image.h, line 276 ERROR: Cannot read file ../gain-reference.mrc It does not exist - Warning: unable to load raw movie frames for MotionCorr/job003/Tiff/EER/GridSquare_11092862/Data/FoilHole_11096245_Data_11093767_11093769_20210911_103042_EER.mrc. Possible reasons include lack of the metadata STAR file, the gain reference and/or the movie. in: /public/EM/RELION/relion-4.0-dev/src/image.h, line 276 ERROR: Cannot read file ../gain-reference.mrc It does not exist - Warning: unable to load raw movie frames for MotionCorr/job003/Tiff/EER/GridSquare_11092862/Data/FoilHole_11096358_Data_11093773_11093775_20210911_103942_EER.mrc. Possible reasons include lack of the metadata STAR file, the gain reference and/or the movie. [hex:4058569] *** Process received signal *** [hex:4058569] Signal: Segmentation fault (11) [hex:4058569] Signal code: Address not mapped (1) [hex:4058569] Failing at address: (nil) [hex:4058569] [ 0] /lib64/libpthread.so.0(+0xf630)[0x14a22c3aa630] [hex:4058569] [ 1] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(_ZN17MicrographHandler9loadMovieERK13MetaDataTableidRSt6vectorI21ParFourierTransformerSaIS4_EEPKS3_IS3_IN6gravis8t2VectorIdEESaISA_EESaISC_EEPSE_di+0x9e0)[0x4af100] [hex:4058569] [ 2] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(_ZN15MotionEstimator14prepMicrographERK13MetaDataTableRSt6vectorI21ParFourierTransformerSaIS4_EERKS3_I5ImageIdESaIS9_EEiRS3_IS3_IS8_I8tComplexIdEESaISG_EESaISI_EERS3_ISB_SaISB_EERS3_IN6gravis8t2VectorIdEESaISR_EERS3_IST_SaIST_EESU_+0x283)[0x519fb3] [hex:4058569] [ 3] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(_ZN15MotionEstimator7processERKSt6vectorI13MetaDataTableSaIS1_EEllb+0x983)[0x51c083] [hex:4058569] [ 4] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(_ZN16MotionRefinerMpi16runWithFccUpdateEv+0x2ae)[0x467ede] [hex:4058569] [ 5] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(main+0x45)[0x436265] [hex:4058569] [ 6] /lib64/libc.so.6(__libc_start_main+0xf5)[0x14a22b30e555] [hex:4058569] [ 7] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi[0x4370ef] [hex:4058569] *** End of error message *** [hex:4058565] *** Process received signal *** [hex:4058565] Signal: Segmentation fault (11) [hex:4058565] Signal code: Address not mapped (1) [hex:4058565] Failing at address: (nil) [hex:4058565] [ 0] /lib64/libpthread.so.0(+0xf630)[0x14f315900630] [hex:4058565] [ 1] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(_ZN17MicrographHandler9loadMovieERK13MetaDataTableidRSt6vectorI21ParFourierTransformerSaIS4_EEPKS3_IS3_IN6gravis8t2VectorIdEESaISA_EESaISC_EEPSE_di+0x9e0)[0x4af100] [hex:4058565] [ 2] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(_ZN15MotionEstimator14prepMicrographERK13MetaDataTableRSt6vectorI21ParFourierTransformerSaIS4_EERKS3_I5ImageIdESaIS9_EEiRS3_IS3_IS8_I8tComplexIdEESaISG_EESaISI_EERS3_ISB_SaISB_EERS3_IN6gravis8t2VectorIdEESaISR_EERS3_IST_SaIST_EESU_+0x283)[0x519fb3] [hex:4058565] [ 3] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(_ZN15MotionEstimator7processERKSt6vectorI13MetaDataTableSaIS1_EEllb+0x983)[0x51c083] [hex:4058565] [ 4] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(_ZN16MotionRefinerMpi16runWithFccUpdateEv+0x2ae)[0x467ede] [hex:4058565] [ 5] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(main+0x45)[0x436265] [hex:4058565] [ 6] /lib64/libc.so.6(__libc_start_main+0xf5)[0x14f314864555] [hex:4058565] [ 7] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi[0x4370ef] [hex:4058565] *** End of error message *** [hex:4058567] *** Process received signal *** [hex:4058567] Signal: Segmentation fault (11) [hex:4058567] Signal code: Address not mapped (1) [hex:4058567] Failing at address: (nil) [hex:4058567] [ 0] /lib64/libpthread.so.0(+0xf630)[0x14b2b884e630] [hex:4058567] [ 1] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(_ZN17MicrographHandler9loadMovieERK13MetaDataTableidRSt6vectorI21ParFourierTransformerSaIS4_EEPKS3_IS3_IN6gravis8t2VectorIdEESaISA_EESaISC_EEPSE_di+0x9e0)[0x4af100] [hex:4058567] [ 2] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(_ZN15MotionEstimator14prepMicrographERK13MetaDataTableRSt6vectorI21ParFourierTransformerSaIS4_EERKS3_I5ImageIdESaIS9_EEiRS3_IS3_IS8_I8tComplexIdEESaISG_EESaISI_EERS3_ISB_SaISB_EERS3_IN6gravis8t2VectorIdEESaISR_EERS3_IST_SaIST_EESU_+0x283)[0x519fb3] [hex:4058567] [ 3] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(_ZN15MotionEstimator7processERKSt6vectorI13MetaDataTableSaIS1_EEllb+0x983)[0x51c083] [hex:4058567] [ 4] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(_ZN16MotionRefinerMpi16runWithFccUpdateEv+0x2ae)[0x467ede] [hex:4058567] [ 5] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(main+0x45)[0x436265] [hex:4058567] [ 6] /lib64/libc.so.6(__libc_start_main+0xf5)[0x14b2b77b2555] [hex:4058567] [ 7] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi[0x4370ef] [hex:4058567] *** End of error message *** [hex:4058568] *** Process received signal *** [hex:4058568] Signal: Segmentation fault (11) [hex:4058568] Signal code: Address not mapped (1) [hex:4058568] Failing at address: (nil) [hex:4058568] [ 0] /lib64/libpthread.so.0(+0xf630)[0x14bf289a8630] [hex:4058568] [ 1] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(_ZN17MicrographHandler9loadMovieERK13MetaDataTableidRSt6vectorI21ParFourierTransformerSaIS4_EEPKS3_IS3_IN6gravis8t2VectorIdEESaISA_EESaISC_EEPSE_di+0x9e0)[0x4af100] [hex:4058568] [ 2] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(_ZN15MotionEstimator14prepMicrographERK13MetaDataTableRSt6vectorI21ParFourierTransformerSaIS4_EERKS3_I5ImageIdESaIS9_EEiRS3_IS3_IS8_I8tComplexIdEESaISG_EESaISI_EERS3_ISB_SaISB_EERS3_IN6gravis8t2VectorIdEESaISR_EERS3_IST_SaIST_EESU_+0x283)[0x519fb3] [hex:4058568] [ 3] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(_ZN15MotionEstimator7processERKSt6vectorI13MetaDataTableSaIS1_EEllb+0x983)[0x51c083] [hex:4058568] [ 4] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(_ZN16MotionRefinerMpi16runWithFccUpdateEv+0x2ae)[0x467ede] [hex:4058568] [ 5] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(main+0x45)[0x436265] [hex:4058568] [ 6] /lib64/libc.so.6(__libc_start_main+0xf5)[0x14bf2790c555] [hex:4058568] [ 7] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi[0x4370ef] [hex:4058568] *** End of error message *** [hex:4058564] *** Process received signal *** [hex:4058564] Signal: Segmentation fault (11) [hex:4058564] Signal code: Address not mapped (1) [hex:4058564] Failing at address: (nil) [hex:4058564] [ 0] /lib64/libpthread.so.0(+0xf630)[0x14a5f38ab630] [hex:4058564] [ 1] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(_ZN17MicrographHandler9loadMovieERK13MetaDataTableidRSt6vectorI21ParFourierTransformerSaIS4_EEPKS3_IS3_IN6gravis8t2VectorIdEESaISA_EESaISC_EEPSE_di+0x9e0)[0x4af100] [hex:4058564] [ 2] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(_ZN15MotionEstimator14prepMicrographERK13MetaDataTableRSt6vectorI21ParFourierTransformerSaIS4_EERKS3_I5ImageIdESaIS9_EEiRS3_IS3_IS8_I8tComplexIdEESaISG_EESaISI_EERS3_ISB_SaISB_EERS3_IN6gravis8t2VectorIdEESaISR_EERS3_IST_SaIST_EESU_+0x283)[0x519fb3] [hex:4058564] [ 3] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(_ZN15MotionEstimator7processERKSt6vectorI13MetaDataTableSaIS1_EEllb+0x983)[0x51c083] [hex:4058564] [ 4] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(_ZN16MotionRefinerMpi16runWithFccUpdateEv+0x2ae)[0x467ede] [hex:4058564] [ 5] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi(main+0x45)[0x436265] [hex:4058564] [ 6] /lib64/libc.so.6(__libc_start_main+0xf5)[0x14a5f280f555] [hex:4058564] [ 7] /public/EM/RELION/relion-4.0-dev/build/bin/relion_motion_refine_mpi[0x4370ef] [hex:4058564] *** End of error message *** WARNING: You did not specify --angpix_ref. The pixel size in the image header of Refine3D/job019/run_half1_class001_unfil.mrc, 0.824 A/px, is used. WARNING: You did not specify --angpix_ref. The pixel size in the image header of Refine3D/job019/run_half1_class001_unfil.mrc, 0.824 A/px, is used. WARNING: You did not specify --angpix_ref. The pixel size in the image header of Refine3D/job019/run_half1_class001_unfil.mrc, 0.824 A/px, is used. WARNING: You did not specify --angpix_ref. The pixel size in the image header of Refine3D/job019/run_half1_class001_unfil.mrc, 0.824 A/px, is used. WARNING: You did not specify --angpix_ref. The pixel size in the image header of Refine3D/job019/run_half1_class001_unfil.mrc, 0.824 A/px, is used. WARNING: You did not specify --angpix_ref. The pixel size in the image header of Refine3D/job019/run_half1_class001_unfil.mrc, 0.824 A/px, is used. [fmb385.lmb.internal:888668] mca_base_component_repository_open: unable to open mca_btl_openib: libosmcomp.so.3: cannot open shared object file: No such file or directory (ignored) [fmb385.lmb.internal:888670] mca_base_component_repository_open: unable to open mca_btl_openib: libosmcomp.so.3: cannot open shared object file: No such file or directory (ignored) [fmb385.lmb.internal:888669] mca_base_component_repository_open: unable to open mca_btl_openib: libosmcomp.so.3: cannot open shared object file: No such file or directory (ignored) [fmb385.lmb.internal:888671] mca_base_component_repository_open: unable to open mca_btl_openib: libosmcomp.so.3: cannot open shared object file: No such file or directory (ignored) WARNING: You did not specify --angpix_ref. The pixel size in the image header of Refine3D/job019/run_half1_class001_unfil.mrc, 0.824 A/px, is used. WARNING: You did not specify --angpix_ref. The pixel size in the image header of Refine3D/job019/run_half1_class001_unfil.mrc, 0.824 A/px, is used. WARNING: You did not specify --angpix_ref. The pixel size in the image header of Refine3D/job019/run_half1_class001_unfil.mrc, 0.824 A/px, is used. WARNING: You did not specify --angpix_ref. The pixel size in the image header of Refine3D/job019/run_half1_class001_unfil.mrc, 0.824 A/px, is used.