SIMPLE test run
| Test step | Program | Duration |
|---|---|---|
| 10_refine3D_auto | refine3D_auto | 7m 36.1s456.1 seconds |
| 9_abinitio3D | abinitio3D | 22m 59.9s1379.9 seconds |
| 8_abinitio3D_cavgs | abinitio3D_cavgs | 7m 20.7s440.7 seconds |
| 7_model_cavgs_rejection | model_cavgs_rejection | 1.5s1.5 seconds |
| 6_abinitio2D | abinitio2D | 3m 53.3s233.3 seconds |
| 5_extract | extract | 5.1s5.1 seconds |
| 4_pick | pick | 1m 37.4s97.4 seconds |
| 3_ctf_estimate | ctf_estimate | 34.2s34.2 seconds |
| 2_motion_correct | motion_correct | 9m 53.3s593.3 seconds |
| 1_import_movies | import_movies | 29.1s29.1 seconds |
Total is the sum of execution times recorded by SIMPLE in this test LOG.
>>> IN-PLANE DIST (DEG) AVG/SDEV/MIN/MAX: 2.884 13.460 0.000 178.364 >>> SHIFT INCR ARG AVG/SDEV/MIN/MAX: 0.315 0.296 0.000 6.360 >>> % SEARCH SPACE SCANNED AVG/SDEV/MIN/MAX: 100.000 0.000 100.000 100.000 >>> MATCHING LOW-PASS LIMIT (THIS ITERATION) 15.127 >>> NU HANDOFF LP (NEXT) AVG/SDEV/MIN/MAX: 11.886 0.000 11.886 11.886 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 17.516 0.000 17.516 17.516 >>> RESOLUTION @ FSC=0.5 AVG/SDEV/MIN/MAX: 19.576 0.000 19.576 19.576 >>> SCORE [0,1] AVG/SDEV/MIN/MAX: 0.457 0.021 0.400 0.555 >>> -------------------- SETTINGS -------------------- >>> | REFINEMENT MODE | prob_neigh >>> | PROB NEIGH MODE | state >>> | NSPACE PROJECTION DIRECTIONS | 20000 >>> | GAU REGULARIZATION | off >>> | ML REGULARIZATION | on, TAU: 1.00000000 >>> | CONICAL REGULARIZATION | off >>> | ICM REGULARIZATION | off >>> | AUTOMASKING | on, MODE: yes >>> | FILTER MODE | nonuniform >>> -------------------------------------------------- >>> CONVERGED: no **** SIMPLE_CALC_GROUP_SIGMAS NORMAL STOP **** **** SIMPLE_REFINE3D NORMAL STOP **** >>> >>> RECONSTRUCTION AT ORIGINAL SAMPLING >>> >>> FINAL RECONSTRUCTION SAMPLING: box=256 smpd= 1.3000 >>> FINAL RECONSTRUCTION: reusing committed canonical sigmas >>> # SHARED-MEMORY THREADS USED BY rec3D MASTER PROCESS: 8 >>> RECONSTRUCT3D: 10 PART(S) COMPLETED IN 4.0 s >>> AUTOMASKING LOW-PASS/DILATION LAYERS/EDGE: 20.00 A/ 6 voxels/ 6 voxels >>> FOUND: 1 CONNECTED COMPONENT(S) >>> FSC MODE: STATE 1, backend=gridding support=sphere posthoc_mask=density phase_randomization=yes >>> FSC AREA SCORE / CONICAL FSC AREA RATIO (cFAR) STATE 1: 0.4180 **** SIMPLE_VOLASSEMBLE NORMAL STOP **** >>> POSTPROCESS: FSC from fsc_state01.bin, 0.5/0.143 at 19.58/ 17.52 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 17.52 A **** SIMPLE_RECONSTRUCT3D NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 456.1 seconds
Recent FSC=0.143 resolution estimates: >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 14.470 0.000 14.470 14.470 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 14.470 0.000 14.470 14.470 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 14.470 0.000 14.470 14.470 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 14.470 0.000 14.470 14.470 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 14.470 0.000 14.470 14.470 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 14.470 0.000 14.470 14.470 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 14.470 0.000 14.470 14.470 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 14.470 0.000 14.470 14.470 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 14.470 0.000 14.470 14.470 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 14.470 0.000 14.470 14.470 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 14.470 0.000 14.470 14.470 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 14.470 0.000 14.470 14.470 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 14.470 0.000 14.470 14.470 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 14.470 0.000 14.470 14.470 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 14.470 0.000 14.470 14.470 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 14.470 0.000 14.470 14.470 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 14.470 0.000 14.470 14.470 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 14.470 0.000 14.470 14.470 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 14.470 0.000 14.470 14.470 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 13.867 0.000 13.867 13.867 Status: **** SIMPLE_VOLASSEMBLE NORMAL STOP **** **** SIMPLE_POSTPROCESS NORMAL STOP **** **** SIMPLE_CALC_GROUP_SIGMAS NORMAL STOP **** **** SIMPLE_REFINE3D NORMAL STOP **** **** SIMPLE_CALC_PSPEC_ASSEMBLE NORMAL STOP **** **** SIMPLE_CALC_PSPEC NORMAL STOP **** **** SIMPLE_VOLASSEMBLE NORMAL STOP **** **** SIMPLE_RECONSTRUCT3D NORMAL STOP **** **** SIMPLE_CALC_GROUP_SIGMAS NORMAL STOP **** **** SIMPLE_REFINE3D NORMAL STOP **** **** SIMPLE_VOLASSEMBLE NORMAL STOP **** **** SIMPLE_RECONSTRUCT3D NORMAL STOP **** **** SIMPLE_BOOTSTRAP_REC3D NORMAL STOP **** **** SIMPLE_ABINITIO3D NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 1379.9 seconds
>>> SIGMA2 INIT: reusing committed canonical state >>> >>> ITERATION 98 >>> **** SIMPLE_CALC_GROUP_SIGMAS NORMAL STOP **** **** SIMPLE_REFINE3D NORMAL STOP **** >>> BOOTSTRAP_REC3D: EUCLID ML-REGULARIZED RECONSTRUCTION ON RESIDUAL SIGMAS, SIGMA ITERATION 99 >>> FSC MODE: STATE 1, backend=gridding support=sphere posthoc_mask=none phase_randomization=no >>> FSC AREA SCORE / CONICAL FSC AREA RATIO (cFAR) STATE 1: 0.0180 **** SIMPLE_VOLASSEMBLE NORMAL STOP **** **** SIMPLE_RECONSTRUCT3D NORMAL STOP **** **** SIMPLE_BOOTSTRAP_REC3D NORMAL STOP **** >>> >>> RE-PROJECTION OF THE FINAL VOLUME >>> >>> GENERATING PROJECTIONS **** SIMPLE_REPROJECT NORMAL STOP **** >>> SHIFTING IMAGES CLASS: 24 RANK: 1 CORR: 0.46 CLASS: 34 RANK: 2 CORR: 0.46 CLASS: 23 RANK: 3 CORR: 0.43 CLASS: 61 RANK: 4 CORR: 0.43 CLASS: 63 RANK: 5 CORR: 0.43 CLASS: 87 RANK: 6 CORR: 0.41 CLASS: 60 RANK: 7 CORR: 0.41 CLASS: 58 RANK: 8 CORR: 0.41 CLASS: 45 RANK: 9 CORR: 0.40 CLASS: 76 RANK: 10 CORR: 0.40 CLASS: 26 RANK: 11 CORR: 0.40 CLASS: 6 RANK: 12 CORR: 0.39 CLASS: 73 RANK: 13 CORR: 0.39 CLASS: 15 RANK: 14 CORR: 0.38 CLASS: 75 RANK: 15 CORR: 0.38 CLASS: 89 RANK: 16 CORR: 0.38 CLASS: 10 RANK: 17 CORR: 0.38 CLASS: 25 RANK: 18 CORR: 0.38 **** SIMPLE_RANK_CAVGS NORMAL STOP **** **** SIMPLE_ABINITIO3D_CAVGS NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 440.7 seconds
>>> PROGRAM: model_cavgs_rejection >>> EXECUTION DIRECTORY: 7_model_cavgs_rejection >>> CAVG QUALITY MODEL : chunk100mics >>> CAVG QUALITY MODEL SOURCE : built-in preset chunk100mics >>> CAVG QUALITY MODEL CONTEXT : chunk >>> CAVG HARD-GATE CONTEXT : chunk >>> CAVG HARD-GATE SOURCE : model artifact >>> DEFAULT HARD GATES REJECTED: 67 >>> CAVG QUALITY SELECTED / REJECTED : 18 / 72 >>> CAVG QUALITY THRESHOLD RAW / OFFSET / EFFECTIVE : 0.350 / 0.000 / 0.350 >>> CAVG QUALITY SEPARATION / USED THRESHOLD : 0.000 USED=T >>> WROTE cavgs_quality_features.txt >>> WROTE quality_selected_cavgs.mrc #CAVGS: 18 >>> WROTE quality_rejected_cavgs.mrc #CAVGS: 72 >>> WROTE hard_gate_rejections.mrc #CAVGS: 67 >>> WROTE quality_ranked_cavgs.mrc #CAVGS: 90 >>> WROTE quality_ranked_cavgs.txt **** SIMPLE_MODEL_CAVGS_REJECTION NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 1.5 seconds
Final class ranking and status: CLASS: 17 RANK: 1 POP: 309 RES: 9.79 CLASS: 51 RANK: 2 POP: 266 RES: 9.79 CLASS: 37 RANK: 3 POP: 330 RES: 10.08 CLASS: 67 RANK: 4 POP: 276 RES: 11.09 CLASS: 31 RANK: 5 POP: 160 RES: 11.48 CLASS: 10 RANK: 6 POP: 208 RES: 11.89 CLASS: 64 RANK: 7 POP: 181 RES: 12.33 CLASS: 89 RANK: 8 POP: 135 RES: 12.80 CLASS: 15 RANK: 9 POP: 157 RES: 12.80 CLASS: 65 RANK: 10 POP: 245 RES: 14.47 CLASS: 87 RANK: 11 POP: 63 RES: 15.13 CLASS: 32 RANK: 12 POP: 99 RES: 15.13 CLASS: 56 RANK: 13 POP: 68 RES: 16.64 CLASS: 73 RANK: 14 POP: 120 RES: 16.64 CLASS: 28 RANK: 15 POP: 30 RES: 17.52 CLASS: 25 RANK: 16 POP: 115 RES: 17.52 CLASS: 27 RANK: 17 POP: 121 RES: 17.52 CLASS: 75 RANK: 18 POP: 134 RES: 18.49 CLASS: 2 RANK: 19 POP: 34 RES: 18.49 CLASS: 6 RANK: 20 POP: 81 RES: 19.58 CLASS: 48 RANK: 21 POP: 39 RES: 19.58 CLASS: 76 RANK: 22 POP: 71 RES: 19.58 CLASS: 42 RANK: 23 POP: 14 RES: 20.80 CLASS: 58 RANK: 24 POP: 89 RES: 20.80 CLASS: 59 RANK: 25 POP: 8 RES: 20.80 CLASS: 60 RANK: 26 POP: 62 RES: 20.80 CLASS: 62 RANK: 27 POP: 33 RES: 22.19 CLASS: 23 RANK: 28 POP: 64 RES: 22.19 CLASS: 81 RANK: 29 POP: 10 RES: 22.19 CLASS: 63 RANK: 30 POP: 34 RES: 25.60 CLASS: 70 RANK: 31 POP: 29 RES: 25.60 CLASS: 3 RANK: 32 POP: 16 RES: 27.73 CLASS: 61 RANK: 33 POP: 29 RES: 30.25 CLASS: 7 RANK: 34 POP: 57 RES: 30.25 CLASS: 34 RANK: 35 POP: 30 RES: 30.25 CLASS: 57 RANK: 36 POP: 26 RES: 30.25 CLASS: 71 RANK: 37 POP: 10 RES: 30.25 CLASS: 47 RANK: 38 POP: 26 RES: 30.25 CLASS: 11 RANK: 39 POP: 35 RES: 30.25 CLASS: 45 RANK: 40 POP: 62 RES: 30.25 CLASS: 88 RANK: 41 POP: 20 RES: 30.25 CLASS: 85 RANK: 42 POP: 34 RES: 30.25 CLASS: 26 RANK: 43 POP: 40 RES: 33.28 CLASS: 24 RANK: 44 POP: 44 RES: 33.28 CLASS: 46 RANK: 45 POP: 19 RES: 33.28 CLASS: 44 RANK: 46 POP: 83 RES: 33.28 CLASS: 41 RANK: 47 POP: 120 RES: 33.28 CLASS: 36 RANK: 48 POP: 118 RES: 33.28 CLASS: 79 RANK: 49 POP: 12 RES: 41.60 CLASS: 77 RANK: 50 POP: 13 RES: 41.60 CLASS: 38 RANK: 51 POP: 19 RES: 41.60 CLASS: 18 RANK: 52 POP: 66 RES: 41.60 CLASS: 52 RANK: 53 POP: 15 RES: 47.54 CLASS: 5 RANK: 54 POP: 99 RES: 47.54 CLASS: 40 RANK: 55 POP: 14 RES: 47.54 CLASS: 4 RANK: 56 POP: 99 RES: 47.54 CLASS: 35 RANK: 57 POP: 61 RES: 47.54 CLASS: 69 RANK: 58 POP: 109 RES: 47.54 CLASS: 68 RANK: 59 POP: 101 RES: 47.54 CLASS: 33 RANK: 60 POP: 99 RES: 47.54 CLASS: 14 RANK: 61 POP: 118 RES: 55.47 CLASS: 22 RANK: 62 POP: 83 RES: 55.47 CLASS: 20 RANK: 63 POP: 98 RES: 55.47 CLASS: 9 RANK: 64 POP: 72 RES: 55.47 CLASS: 86 RANK: 65 POP: 65 RES: 55.47 CLASS: 29 RANK: 66 POP: 97 RES: 66.56 CLASS: 54 RANK: 67 POP: 106 RES: 66.56 CLASS: 53 RANK: 68 POP: 109 RES: 66.56 CLASS: 1 RANK: 69 POP: 92 RES: 66.56 CLASS: 50 RANK: 70 POP: 19 RES: 66.56 CLASS: 12 RANK: 71 POP: 121 RES: 66.56 CLASS: 43 RANK: 72 POP: 52 RES: 66.56 CLASS: 21 RANK: 73 POP: 36 RES: 66.56 CLASS: 83 RANK: 74 POP: 100 RES: 66.56 CLASS: 72 RANK: 75 POP: 6 RES: 66.56 CLASS: 16 RANK: 76 POP: 9 RES: 66.56 CLASS: 30 RANK: 77 POP: 100 RES: 83.20 CLASS: 13 RANK: 78 POP: 85 RES: 83.20 CLASS: 49 RANK: 79 POP: 105 RES: 83.20 CLASS: 84 RANK: 80 POP: 87 RES: 83.20 CLASS: 82 RANK: 81 POP: 107 RES: 83.20 CLASS: 80 RANK: 82 POP: 128 RES: 83.20 CLASS: 19 RANK: 83 POP: 116 RES: 83.20 CLASS: 74 RANK: 84 POP: 91 RES: 83.20 CLASS: 66 RANK: 85 POP: 96 RES: 83.20 CLASS: 8 RANK: 86 POP: 68 RES: 83.20 CLASS: 90 RANK: 87 POP: 107 RES: 110.93 CLASS: 39 RANK: 88 POP: 124 RES: 110.93 CLASS: 78 RANK: 89 POP: 9 RES: 166.40 Status: **** SIMPLE_CAVGASSEMBLE NORMAL STOP **** **** SIMPLE_CALC_GROUP_SIGMAS NORMAL STOP **** **** SIMPLE_PROB_ALIGN2D NORMAL STOP **** **** SIMPLE_CAVGASSEMBLE NORMAL STOP **** **** SIMPLE_CALC_GROUP_SIGMAS NORMAL STOP **** **** SIMPLE_CLUSTER2D NORMAL STOP **** **** SIMPLE_CAVGASSEMBLE NORMAL STOP **** **** SIMPLE_DISTR_MAKE_CAVGS NORMAL STOP **** **** SIMPLE_RANK_CAVGS NORMAL STOP **** **** SIMPLE_ABINITIO2D NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 233.3 seconds
100. percent micrographs marker not found; recent extract diagnostics: >>> EXTRACT: 5 PART(S) COMPLETED IN 4.0 s **** SIMPLE_EXTRACT_DISTR NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 5.1 seconds
100. percent micrographs marker not found; recent pick diagnostics: >>> PICK: 5 PART(S) COMPLETED IN 97.0 s **** SIMPLE_DISTR_PICK NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 97.4 seconds
100. percent marker not found; recent CTF diagnostics: >>> CTF_ESTIMATE: 5 PART(S) COMPLETED IN 34.0 s **** SIMPLE_DISTR_CTF_ESTIMATE NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 34.2 seconds
100. percent marker not found; recent motion-correction diagnostics: **** SIMPLE_DISTR_MOTION_CORRECT NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 593.3 seconds
>>> IMPORTED 100 MOVIE(S) >>> TOTAL NUMBER OF MOVIE(S): 100 **** IMPORT_MOVIES NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 29.1 seconds