SIMPLE Test Report - test_simulated_workflow_1jxy
SIMPLE test run
Execution times
13m 54.7sTotal across 1 timed test step
| Test step | Program | Duration |
|---|---|---|
| simulated_workflow/7_abinitio3D | workflow | 13m 54.7s834.7 seconds |
Total is the sum of execution times recorded by SIMPLE in this test LOG.
simulated_workflow/7_abinitio3D13m 54.7s
orientations_distribution_state01.jpg
orientations_distribution_state01_stage01.jpg
orientations_distribution_state01_stage02.jpg
orientations_distribution_state01_stage03.jpg
orientations_distribution_state01_stage04.jpg
orientations_distribution_state01_stage05.jpg
orientations_distribution_state01_stage06.jpg
orientations_distribution_state01_stage07.jpg
orientations_distribution_state01_stage08.jpg
orthogonal_reprojs_state01.jpg
orthogonal_reprojs_state01_stage01.jpg
orthogonal_reprojs_state01_stage02.jpg
orthogonal_reprojs_state01_stage03.jpg
orthogonal_reprojs_state01_stage04.jpg
orthogonal_reprojs_state01_stage05.jpg
orthogonal_reprojs_state01_stage06.jpg
orthogonal_reprojs_state01_stage07.jpg
orthogonal_reprojs_state01_stage08.jpg
LOG summary: PROGRAM workflow
>>> NU BANK CAP: FSC=0.143 16.640 A; candidates finer than 10.852 A dropped; 3 candidates retained of 8 static labels
>>> NU AUXILIARY MEMBER: ML-regularized pair at 16.640 A is within the ladder (finest rung 11.886 A); the rungs compete alone
>>> NU LOW-PASS ASSIGNMENTS (retained filter bank)
Analyzed voxels: 1389223
Source Bank Fourier k LP limit (A) Voxels Pct mask
Base 1 12 20.800 1389223 100.00%
Base 2 17 14.682 0 0.00%
Base 3 21 11.886 0 0.00%
>>> NU MATCHING LOW-PASS HANDOFF: STATE 1, 11.89 A (finest bank member; finest label with 1% of signal voxels 20.80 A, raw finest label 20.80 A)
**** SIMPLE_VOLASSEMBLE NORMAL STOP ****
**** SIMPLE_RECONSTRUCT3D NORMAL STOP ****
>>> BOOTSTRAP_REC3D: RESIDUAL SIGMA2 PASS AGAINST THE BOOTSTRAP MAP, ITERATION 135
>>> SIGMA2 INIT: reusing committed canonical state
>>>
>>> ITERATION 135
>>>
>>> NU filter matching low-pass limit: 11.886 A
>>> NU filter promoted matching low-pass to command line: 11.886 A
**** SIMPLE_CALC_GROUP_SIGMAS NORMAL STOP ****
**** SIMPLE_REFINE3D NORMAL STOP ****
>>> BOOTSTRAP_REC3D: EUCLID ML-REGULARIZED RECONSTRUCTION ON RESIDUAL SIGMAS, SIGMA ITERATION 136
>>> FSC MODE: STATE 1, backend=gridding support=sphere posthoc_mask=none phase_randomization=no
>>> FSC AREA SCORE / CONICAL FSC AREA RATIO (cFAR) STATE 1: 0.0000
**** SIMPLE_VOLASSEMBLE NORMAL STOP ****
>>> POSTPROCESS: FSC from fsc_state01.bin, 0.5/0.143 at 22.69/ 13.14 A
>>> POSTPROCESS: ML-regularized map (solve_kind=gridding_regularized), its prior already FSC-weighted it: no FSC weighting
>>> POSTPROCESS: B-sharpened, then Butterworth low-pass at 13.14 A
**** SIMPLE_RECONSTRUCT3D NORMAL STOP ****
**** SIMPLE_BOOTSTRAP_REC3D NORMAL STOP ****
>>> ABINITIO3D RUN MANIFEST WRITTEN: abinitio3D_20260929T022045.075_3305157
**** SIMPLE_ABINITIO3D NORMAL STOP ****
>>> Simulated truth dimensions/sampling: 192 192 192 / 1.300
>>> Final volume dimensions/sampling: 192 192 192 / 1.300
>>> workflow_reconstruction docking correlation: direct= 0.9616, mirrored= 0.8746
>>> Registered whole-volume Pearson correlation: 0.8139; minimum 0.2000
>>> Masked truth FSC: 0.500 at 14.68 A; 0.143 at 8.05 A; maximum 40.00 A
PASS: simulated_workflow 1jxy whole-volume correlation= 0.8139, FSC=0.143 at 8.05 A
**** SIMPLE_TEST_SIMULATED_WORKFLOW NORMAL STOP ****
**** SIMPLE Git Commit: 3cad71a1
**** Execution time: 834.7 seconds
simulated_workflow/6_abinitio2D
cavgs_iter024.jpg
LOG summary: PROGRAM workflow
**** SIMPLE_PROB_TAB2D NORMAL STOP **** >>> PROB_ALIGN2D: prob_tab2D workers completed; merging partition tables >>> PROB_ALIGN2D: running global probabilistic assignment >>> PROB_TAB2D_ASSIGN: preparing 66 particles x 4 >>> PROB_TAB2D_ASSIGN: using likelihood weights exp(-dist) >>> PROB_TAB2D_ASSIGN: sorting per-class particle distances >>> PROB_TAB2D_ASSIGN: assigning particles >>> PROB_TAB2D_ASSIGN: done >>> PROB_ALIGN2D: writing assignment assignment_part.dat >>> PROB_ALIGN2D: assignment written **** SIMPLE_PROB_ALIGN2D NORMAL STOP **** >>> CLASS OVERLAP: 1.000 >>> % PARTICLES SAMPLED THIS ITERATION 100.000 (66/66) >>> % PARTICLES UPDATED SO FAR 100.000 >>> % PARTICLES USED FOR AVERAGING 100.000 >>> % CONTINUOUS IN-PLANE RUNS IMPROVED 100.000 (66 attempts) >>> IN-PLANE DIST (DEG) AVG/SDEV/MIN/MAX: 0.467 0.791 0.000 1.800 >>> SHIFT INCR ARG AVG/SDEV/MIN/MAX: 0.281 0.220 0.024 1.450 >>> % SEARCH SPACE SCANNED AVG/SDEV/MIN/MAX: 100.000 0.000 100.000 100.000 >>> MATCHING LOW-PASS LIMIT AVG/SDEV/MIN/MAX: 14.682 0.000 14.682 14.682 >>> ESTIMATED LOW-PASS LIMIT AVG/SDEV/MIN/MAX: 0.000 0.000 0.000 0.000 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 8.052 0.000 8.052 8.052 >>> SCORE [0,1] AVG/SDEV/MIN/MAX: 0.444 0.024 0.398 0.506 >>> -------------------- SETTINGS -------------------- >>> | REFINEMENT MODE | prob >>> | PROB NEIGH MODE | state >>> | GAU REGULARIZATION | off >>> | ML REGULARIZATION | on, TAU: 1.00000000 >>> | FILTER MODE | none >>> -------------------------------------------------- >>> CONVERGED: .YES. **** SIMPLE_CALC_GROUP_SIGMAS NORMAL STOP **** >>> JPEG /usr/local/cache/actions-runner/_work/SIMPLE_data_testing/SIMPLE_data_testing/test_simulated_workflow_1jxy/simulated_workflow/6_abinitio2D/cavgs_iter024.jpg **** SIMPLE_CLUSTER2D NORMAL STOP **** >>> MAKE_CAVGS RAW_SOURCE: oritype=ptcl2D particles=1-66 stack=/usr/local/cache/actions-runner/_work/SIMPLE_data_testing/SIMPLE_data_testing/test_simulated_workflow_1jxy/simulated_workflow/5_extract/ptcls_from_simulate_movie_001_intg.mrcs indstk(first)=1 **** SIMPLE_MAKE_CAVGS NORMAL STOP **** CLASS: 1 RANK: 1 POP: 66 RES: 7.80 **** SIMPLE_RANK_CAVGS NORMAL STOP **** **** SIMPLE_ABINITIO2D NORMAL STOP **** >>> Step 10: ab initio 3D
simulated_workflow/5_extract
ptcls_sample.jpg
ptcls_sample_lp.jpg
LOG summary: PROGRAM workflow
>>> EXECUTION DIRECTORY: 5_extract >>> EXTRACT: 1 PART(S) COMPLETED IN 2.0 s >>> BAND-PASS FILTERING IMAGES **** SIMPLE_EXTRACT_DISTR NORMAL STOP **** >>> Step 9: ab initio 2D
simulated_workflow/4_pick
LOG summary: PROGRAM workflow
>>> EXECUTION DIRECTORY: 4_pick >>> PICK: 1 PART(S) COMPLETED IN 30.0 s **** SIMPLE_DISTR_PICK NORMAL STOP **** >>> Step 8: particle extraction
simulated_workflow/3_ctf_estimate
simulate_movie_001_ctf_estimate_diag.jpg
simulate_movie_002_ctf_estimate_diag.jpg
simulate_movie_003_ctf_estimate_diag.jpg
simulate_movie_004_ctf_estimate_diag.jpg
simulate_movie_005_ctf_estimate_diag.jpg
simulate_movie_006_ctf_estimate_diag.jpg
simulate_movie_007_ctf_estimate_diag.jpg
simulate_movie_008_ctf_estimate_diag.jpg
simulate_movie_009_ctf_estimate_diag.jpg
simulate_movie_010_ctf_estimate_diag.jpg
LOG summary: PROGRAM workflow
>>> EXECUTION DIRECTORY: 3_ctf_estimate >>> CTF_ESTIMATE: 1 PART(S) COMPLETED IN 21.0 s **** SIMPLE_DISTR_CTF_ESTIMATE NORMAL STOP **** >>> Step 7: particle picking with segdiam
2_simulate_movies
LOG summary: PROGRAM simulate_movies
>>> GENERATING MOVIE FRAMES >>> GENERATING OPTIMAL AVERAGE **** SIMPLE_SIMULATE_MOVIE NORMAL STOP **** Fraction of area occupied by ptcls: 0.156 >>> GENERATING PARTICLE POSITIONS >>> GENERATING MOVIE FRAMES >>> GENERATING OPTIMAL AVERAGE **** SIMPLE_SIMULATE_MOVIE NORMAL STOP **** Fraction of area occupied by ptcls: 0.156 >>> GENERATING PARTICLE POSITIONS >>> GENERATING MOVIE FRAMES >>> GENERATING OPTIMAL AVERAGE **** SIMPLE_SIMULATE_MOVIE NORMAL STOP **** Fraction of area occupied by ptcls: 0.156 >>> GENERATING PARTICLE POSITIONS >>> GENERATING MOVIE FRAMES >>> GENERATING OPTIMAL AVERAGE **** SIMPLE_SIMULATE_MOVIE NORMAL STOP **** Fraction of area occupied by ptcls: 0.156 >>> GENERATING PARTICLE POSITIONS >>> GENERATING MOVIE FRAMES >>> GENERATING OPTIMAL AVERAGE **** SIMPLE_SIMULATE_MOVIE NORMAL STOP **** Fraction of area occupied by ptcls: 0.156 >>> GENERATING PARTICLE POSITIONS >>> GENERATING MOVIE FRAMES >>> GENERATING OPTIMAL AVERAGE **** SIMPLE_SIMULATE_MOVIE NORMAL STOP **** Fraction of area occupied by ptcls: 0.156 >>> GENERATING PARTICLE POSITIONS >>> GENERATING MOVIE FRAMES >>> GENERATING OPTIMAL AVERAGE **** SIMPLE_SIMULATE_MOVIE NORMAL STOP **** Fraction of area occupied by ptcls: 0.156 >>> GENERATING PARTICLE POSITIONS >>> GENERATING MOVIE FRAMES >>> GENERATING OPTIMAL AVERAGE **** SIMPLE_SIMULATE_MOVIE NORMAL STOP **** >>> Step 4: create a project and import the movies **** NEW_PROJECT NORMAL STOP ****
simulated_workflow/2_motion_correct
simulate_movie_001_thumb.jpg
simulate_movie_002_thumb.jpg
simulate_movie_003_thumb.jpg
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simulate_movie_005_thumb.jpg
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simulate_movie_007_thumb.jpg
simulate_movie_008_thumb.jpg
simulate_movie_009_thumb.jpg
simulate_movie_010_thumb.jpg
LOG summary: PROGRAM workflow
>>> EXECUTION DIRECTORY: 2_motion_correct >>> MOTION_CORRECT: 1 PART(S) COMPLETED IN 32.0 s **** SIMPLE_DISTR_MOTION_CORRECT NORMAL STOP **** >>> Step 6: CTF estimation
1_reproject
LOG summary: PROGRAM reproject
>>> Step 1: create a volume from 1jxy
Sampling distance: 1.300 Angstrom
Bounding box(Angstrom) x: -57.64 - 57.97
y: -70.50 - 67.67
z: -87.47 - 82.66
WARNING! PDB atomic center off of the center volume; check_center; \simple_atoms.f90; line: 1370
Atomic center at -0.0, -2.3, -2.4 (center of volume at 0, 0, 0)
WARNING! PDB atomic center moved to the center of the box; center_pdbcoord; \simple_atoms.f90; line: 1414
3D MRC simulated volume created ( 192 192 192 ) voxels
>>> Step 2: generate well-spaced spiral reprojections
>>> EXECUTION DIRECTORY: 1_reproject
>>> GENERATING PROJECTIONS
**** SIMPLE_REPROJECT NORMAL STOP ****
>>> Step 3: generate 10 simulated movies with 16 frames and 10 random projections each
simulated_workflow/1_import_movies
movthumb1.jpg
LOG summary: PROGRAM workflow
>>> EXECUTION DIRECTORY: 1_import_movies >>> IMPORTED 10 MOVIE(S) >>> TOTAL NUMBER OF MOVIE(S): 10 **** IMPORT_MOVIES NORMAL STOP **** >>> Step 5: motion correction