jacob-r-anderson
commented
10 months ago I have looked more closely at the output files. It appears that the error is likely because the references generated after the first iteration contain NaNs. Unclear why this is occuring now and not before.
Again - this is a problem where a job that did not throw an error now throws an error. The exact data input are identical as shown above.
_After the first iteration, run_it001_half1class001.mrc has NaNs.
header run_it001_half1_class001.mrc
RO image file on unit 1 : run_it001_half1_class001.mrc Size= 153532 K
Number of columns, rows, sections ..... 340 340 340
Map mode .............................. 2 (32-bit real)
Start cols, rows, sects, grid x,y,z ... 0 0 0 340 340 340
Pixel spacing (Angstroms).............. 3.360 3.360 3.360
Cell angles ........................... 90.000 90.000 90.000
Fast, medium, slow axes ............... X Y Z
Origin on x,y,z ....................... 0.000 0.000 0.000
Minimum density ....................... NaN
Maximum density ....................... NaN
Mean density .......................... NaN
tilt angles (original,current) ........ 0.0 0.0 0.0 0.0 0.0 0.0
Space group,# extra bytes,idtype,lens . 0 0 0 0
1 Titles :
Relion 09-Jan-24 13:40:28 Compared to:
RO image file on unit 1 : run_it000_half1_class001.mrc Size= 153532 K
Number of columns, rows, sections ..... 340 340 340
Map mode .............................. 2 (32-bit real)
Start cols, rows, sects, grid x,y,z ... 0 0 0 340 340 340
Pixel spacing (Angstroms).............. 3.360 3.360 3.360
Cell angles ........................... 90.000 90.000 90.000
Fast, medium, slow axes ............... X Y Z
Origin on x,y,z ....................... 0.000 0.000 0.000
Minimum density ....................... -0.20950
Maximum density ....................... 0.20464
Mean density .......................... 0.53888E-12
RMS deviation from mean................ 0.28042E-01
tilt angles (original,current) ........ 0.0 0.0 0.0 0.0 0.0 0.0
Space group,# extra bytes,idtype,lens . 0 0 0 0
Describe your problem
I have been using Relion 4.0.1 Pseudosubtomogram pipeline for a large dataset for several months. Despite having jobs succeed in the past with identical inputs, I have now invariable come across the error below issue. The error reproducibly occurs immediately after the first iteration. A similar post was made for 2DC in 2018, however the troubleshooting there did not solve this problem.
Bizarrely, I even see this problem if I use the EXACT same parameters from jobs run two months ago, but ones that did not throw the error.
What would cause an error to be thrown now, and not then, with identical parameters and inputs?
Environment:
Dataset:
Job options:
note.txtin the job directory):Example of a command that tripped an error:
which relion_refine_mpi--o Refine3D/job1155/run --auto_refine --split_random_halves --ios ReconstructParticleTomo/job915/optimisation_set.star --solvent_correct_fsc --ref ReconstructParticleTomo/job915/merged.mrc --firstiter_cc --ini_high 40 --dont_combine_weights_via_disc --pool 3 --pad 1 --auto_ignore_angles --auto_resol_angles --ctf --particle_diameter 2000 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 5 --auto_local_healpix_order 5 --offset_range 4 --offset_step 2 --sym C1 --low_resol_join_halves 40 --norm --scale --j 4 --gpu "" --pipeline_control Refine3D/job1155/`Example of the same command that did not trip an error:
which relion_refine_mpi--o Refine3D/job916/run --auto_refine --split_random_halves --ios ReconstructParticleTomo/job915/optimisation_set.star --solvent_correct_fsc --ref ReconstructParticleTomo/job915/merged.mrc --firstiter_cc --ini_high 40 --dont_combine_weights_via_disc --pool 3 --pad 1 --auto_ignore_angles --auto_resol_angles --ctf --particle_diameter 2000 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 5 --auto_local_healpix_order 5 --offset_range 4 --offset_step 2 --sym C1 --low_resol_join_halves 40 --norm --scale --j 4 --gpu "" --pipeline_control Refine3D/job916/`Error message: