SIMPLE test run
| Test step | Program | Duration |
|---|---|---|
| 10_refine3D_auto | refine3D_auto | 22m 21.0s1341.0 seconds |
| 9_abinitio3D | abinitio3D | 15m 10.6s910.6 seconds |
| 8_abinitio3D_cavgs | abinitio3D_cavgs | 8m 47.2s527.2 seconds |
| 7_model_cavgs_rejection | model_cavgs_rejection | 1.6s1.6 seconds |
| 6_abinitio2D | abinitio2D | 3m 57.5s237.5 seconds |
| 5_extract | extract | 5.4s5.4 seconds |
| 4_pick | pick | 1m 30.3s90.3 seconds |
| 3_ctf_estimate | ctf_estimate | 50.3s50.3 seconds |
| 2_motion_correct | motion_correct | 10m 45.5s645.5 seconds |
| 1_import_movies | import_movies | 16.6s16.6 seconds |
Total is the sum of execution times recorded by SIMPLE in this test LOG.
>>> % GREEDY SEARCHES 0.000 >>> DIST BTW BEST ORIS (DEG) AVG/SDEV/MIN/MAX: 2.127 5.028 0.018 117.074 >>> IN-PLANE DIST (DEG) AVG/SDEV/MIN/MAX: 1.452 6.789 0.000 166.909 >>> SHIFT INCR ARG AVG/SDEV/MIN/MAX: 0.252 0.237 0.000 2.871 >>> % SEARCH SPACE SCANNED AVG/SDEV/MIN/MAX: 100.000 0.000 100.000 100.000 >>> MATCHING LOW-PASS LIMIT AVG/SDEV/MIN/MAX: 4.010 0.000 4.010 4.010 >>> ESTIMATED LOW-PASS LIMIT AVG/SDEV/MIN/MAX: 0.000 0.000 0.000 0.000 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 12.800 0.000 12.800 12.800 >>> SCORE [0,1] AVG/SDEV/MIN/MAX: 0.373 0.002 0.370 0.382 >>> -------------------- 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_REFINE3D NORMAL STOP **** >>> # SHARED-MEMORY THREADS USED BY rec3D MASTER PROCESS: 8 **** Execution time: 2.3 seconds **** Execution time: 2.4 seconds **** Execution time: 2.5 seconds **** Execution time: 2.6 seconds **** Execution time: 2.6 seconds **** Execution time: 2.7 seconds **** Execution time: 2.7 seconds **** Execution time: 2.7 seconds **** Execution time: 2.8 seconds **** Execution time: 2.8 seconds >>> FSC AREA SCORE / CONICAL FSC AREA RATIO (cFAR) STATE 1: 0.3906 >>> AUTOMASKING >>> FOUND: 109 CONNECTED COMPONENT(S) **** SIMPLE_VOLASSEMBLE NORMAL STOP **** **** SIMPLE_RECONSTRUCT3D NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 1341.0 seconds
Recent FSC=0.143 resolution estimates: >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 13.867 0.000 13.867 13.867 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 14.470 0.000 14.470 14.470 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 13.312 0.000 13.312 13.312 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 12.800 0.000 12.800 12.800 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 12.800 0.000 12.800 12.800 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 12.800 0.000 12.800 12.800 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 12.800 0.000 12.800 12.800 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 12.800 0.000 12.800 12.800 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 12.800 0.000 12.800 12.800 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 12.326 0.000 12.326 12.326 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 11.886 0.000 11.886 11.886 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 11.886 0.000 11.886 11.886 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 11.093 0.000 11.093 11.093 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 11.093 0.000 11.093 11.093 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 10.735 0.000 10.735 10.735 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 10.735 0.000 10.735 10.735 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 10.735 0.000 10.735 10.735 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 10.735 0.000 10.735 10.735 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 10.735 0.000 10.735 10.735 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 10.735 0.000 10.735 10.735 Status: **** Execution time: 2.1 seconds **** Execution time: 2.5 seconds **** Execution time: 2.5 seconds **** Execution time: 2.5 seconds **** Execution time: 2.5 seconds **** Execution time: 2.6 seconds **** Execution time: 2.6 seconds **** Execution time: 2.7 seconds **** Execution time: 2.7 seconds **** Execution time: 2.7 seconds **** SIMPLE_VOLASSEMBLE NORMAL STOP **** **** SIMPLE_RECONSTRUCT3D NORMAL STOP **** **** SIMPLE_BOOTSTRAP_REC3D NORMAL STOP **** **** SIMPLE_ABINITIO3D NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 910.6 seconds
>>> BOOTSTRAP_REC3D WROTE SIGMA STAR: sigma2_it_97.star >>> BOOTSTRAP_REC3D PASS 2: EUCLID ML-REGULARIZED RECONSTRUCTION >>> FSC AREA SCORE / CONICAL FSC AREA RATIO (cFAR) STATE 1: 0.0325 **** 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: 28 RANK: 1 CORR: 0.39 CLASS: 12 RANK: 2 CORR: 0.38 CLASS: 1 RANK: 3 CORR: 0.38 CLASS: 79 RANK: 4 CORR: 0.38 CLASS: 73 RANK: 5 CORR: 0.38 CLASS: 34 RANK: 6 CORR: 0.37 CLASS: 51 RANK: 7 CORR: 0.37 CLASS: 3 RANK: 8 CORR: 0.37 CLASS: 52 RANK: 9 CORR: 0.37 CLASS: 54 RANK: 10 CORR: 0.37 CLASS: 37 RANK: 11 CORR: 0.37 CLASS: 49 RANK: 12 CORR: 0.37 CLASS: 25 RANK: 13 CORR: 0.37 CLASS: 33 RANK: 14 CORR: 0.37 CLASS: 69 RANK: 15 CORR: 0.37 CLASS: 23 RANK: 16 CORR: 0.37 CLASS: 15 RANK: 17 CORR: 0.37 CLASS: 61 RANK: 18 CORR: 0.37 CLASS: 18 RANK: 19 CORR: 0.37 CLASS: 84 RANK: 20 CORR: 0.37 CLASS: 16 RANK: 21 CORR: 0.37 CLASS: 29 RANK: 22 CORR: 0.37 CLASS: 35 RANK: 23 CORR: 0.36 CLASS: 71 RANK: 24 CORR: 0.35 **** SIMPLE_RANK_CAVGS NORMAL STOP **** **** SIMPLE_ABINITIO3D_CAVGS NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 527.2 seconds
>>> PROGRAM: model_cavgs_rejection >>> EXECUTION DIRECTORY: 7_model_cavgs_rejection >>> CAVG QUALITY MODEL : chunk100mics >>> CAVG QUALITY CONTEXT : chunk >>> DEFAULT HARD GATES REJECTED: 64 >>> CAVG QUALITY SELECTED / REJECTED : 24 / 66 >>> 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: 24 >>> WROTE quality_rejected_cavgs.mrc #CAVGS: 66 >>> WROTE hard_gate_rejections.mrc #CAVGS: 64 >>> WROTE quality_ranked_cavgs.mrc #CAVGS: 90 >>> WROTE quality_ranked_cavgs.txt **** SIMPLE_MODEL_CAVGS_REJECTION NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 1.6 seconds
Final class ranking and status: CLASS: 24 RANK: 1 POP: 283 RES: 10.08 CLASS: 60 RANK: 2 POP: 122 RES: 11.89 CLASS: 10 RANK: 3 POP: 133 RES: 12.80 CLASS: 43 RANK: 4 POP: 266 RES: 13.87 CLASS: 12 RANK: 5 POP: 65 RES: 13.87 CLASS: 34 RANK: 6 POP: 187 RES: 15.13 CLASS: 56 RANK: 7 POP: 10 RES: 15.85 CLASS: 61 RANK: 8 POP: 176 RES: 15.85 CLASS: 14 RANK: 9 POP: 171 RES: 16.64 CLASS: 39 RANK: 10 POP: 264 RES: 16.64 CLASS: 15 RANK: 11 POP: 176 RES: 16.64 CLASS: 18 RANK: 12 POP: 125 RES: 16.64 CLASS: 28 RANK: 13 POP: 66 RES: 16.64 CLASS: 51 RANK: 14 POP: 139 RES: 17.52 CLASS: 3 RANK: 15 POP: 112 RES: 17.52 CLASS: 49 RANK: 16 POP: 136 RES: 17.52 CLASS: 23 RANK: 17 POP: 182 RES: 18.49 CLASS: 54 RANK: 18 POP: 112 RES: 18.49 CLASS: 64 RANK: 19 POP: 24 RES: 19.58 CLASS: 13 RANK: 20 POP: 15 RES: 20.80 CLASS: 80 RANK: 21 POP: 41 RES: 20.80 CLASS: 16 RANK: 22 POP: 131 RES: 20.80 CLASS: 70 RANK: 23 POP: 5 RES: 20.80 CLASS: 25 RANK: 24 POP: 58 RES: 22.19 CLASS: 48 RANK: 25 POP: 143 RES: 22.19 CLASS: 33 RANK: 26 POP: 153 RES: 22.19 CLASS: 69 RANK: 27 POP: 112 RES: 22.19 CLASS: 29 RANK: 28 POP: 46 RES: 23.77 CLASS: 79 RANK: 29 POP: 71 RES: 23.77 CLASS: 19 RANK: 30 POP: 8 RES: 25.60 CLASS: 73 RANK: 31 POP: 33 RES: 25.60 CLASS: 67 RANK: 32 POP: 11 RES: 25.60 CLASS: 75 RANK: 33 POP: 7 RES: 27.73 CLASS: 52 RANK: 34 POP: 61 RES: 27.73 CLASS: 71 RANK: 35 POP: 47 RES: 27.73 CLASS: 4 RANK: 36 POP: 24 RES: 27.73 CLASS: 37 RANK: 37 POP: 36 RES: 30.25 CLASS: 35 RANK: 38 POP: 51 RES: 30.25 CLASS: 84 RANK: 39 POP: 43 RES: 30.25 CLASS: 72 RANK: 40 POP: 126 RES: 33.28 CLASS: 68 RANK: 41 POP: 19 RES: 33.28 CLASS: 1 RANK: 42 POP: 40 RES: 36.98 CLASS: 82 RANK: 43 POP: 18 RES: 36.98 CLASS: 22 RANK: 44 POP: 7 RES: 41.60 CLASS: 42 RANK: 45 POP: 16 RES: 41.60 CLASS: 5 RANK: 46 POP: 96 RES: 41.60 CLASS: 65 RANK: 47 POP: 110 RES: 41.60 CLASS: 62 RANK: 48 POP: 15 RES: 47.54 CLASS: 59 RANK: 49 POP: 45 RES: 47.54 CLASS: 7 RANK: 50 POP: 89 RES: 47.54 CLASS: 88 RANK: 51 POP: 16 RES: 47.54 CLASS: 50 RANK: 52 POP: 130 RES: 47.54 CLASS: 11 RANK: 53 POP: 77 RES: 47.54 CLASS: 45 RANK: 54 POP: 45 RES: 47.54 CLASS: 21 RANK: 55 POP: 83 RES: 47.54 CLASS: 20 RANK: 56 POP: 97 RES: 47.54 CLASS: 40 RANK: 57 POP: 80 RES: 47.54 CLASS: 41 RANK: 58 POP: 76 RES: 47.54 CLASS: 8 RANK: 59 POP: 61 RES: 47.54 CLASS: 30 RANK: 60 POP: 92 RES: 55.47 CLASS: 55 RANK: 61 POP: 55 RES: 55.47 CLASS: 6 RANK: 62 POP: 8 RES: 55.47 CLASS: 47 RANK: 63 POP: 71 RES: 55.47 CLASS: 85 RANK: 64 POP: 9 RES: 55.47 CLASS: 81 RANK: 65 POP: 114 RES: 55.47 CLASS: 76 RANK: 66 POP: 121 RES: 55.47 CLASS: 74 RANK: 67 POP: 79 RES: 55.47 CLASS: 63 RANK: 68 POP: 88 RES: 66.56 CLASS: 89 RANK: 69 POP: 16 RES: 66.56 CLASS: 44 RANK: 70 POP: 12 RES: 66.56 CLASS: 83 RANK: 71 POP: 8 RES: 66.56 CLASS: 78 RANK: 72 POP: 106 RES: 66.56 CLASS: 38 RANK: 73 POP: 90 RES: 66.56 CLASS: 31 RANK: 74 POP: 87 RES: 83.20 CLASS: 57 RANK: 75 POP: 81 RES: 83.20 CLASS: 53 RANK: 76 POP: 96 RES: 83.20 CLASS: 90 RANK: 77 POP: 18 RES: 83.20 CLASS: 87 RANK: 78 POP: 99 RES: 83.20 CLASS: 77 RANK: 79 POP: 68 RES: 83.20 CLASS: 36 RANK: 80 POP: 81 RES: 83.20 CLASS: 17 RANK: 81 POP: 117 RES: 83.20 CLASS: 66 RANK: 82 POP: 57 RES: 83.20 CLASS: 32 RANK: 83 POP: 100 RES: 83.20 CLASS: 27 RANK: 84 POP: 66 RES: 110.93 CLASS: 26 RANK: 85 POP: 69 RES: 110.93 CLASS: 2 RANK: 86 POP: 103 RES: 110.93 CLASS: 58 RANK: 87 POP: 47 RES: 166.40 CLASS: 86 RANK: 88 POP: 5 RES: 166.40 CLASS: 46 RANK: 89 POP: 3 RES: 331.50 Status: **** SIMPLE_MAKE_CAVGS NORMAL STOP **** **** Execution time: 3.4 seconds **** SIMPLE_MAKE_CAVGS NORMAL STOP **** **** Execution time: 3.5 seconds **** SIMPLE_MAKE_CAVGS NORMAL STOP **** **** Execution time: 3.6 seconds **** SIMPLE_CAVGASSEMBLE NORMAL STOP **** **** SIMPLE_DISTR_MAKE_CAVGS NORMAL STOP **** **** SIMPLE_RANK_CAVGS NORMAL STOP **** **** SIMPLE_ABINITIO2D NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 237.5 seconds
Lines after the last 100. percent of the micrographs processed: **** SIMPLE_EXTRACT NORMAL STOP **** **** Execution time: 3.1 seconds **** SIMPLE_EXTRACT_DISTR NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 5.4 seconds
Lines after the last 100. percent of the micrographs processed: **** SIMPLE_PICK NORMAL STOP **** **** Execution time: 88.9 seconds **** SIMPLE_DISTR_PICK NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 90.3 seconds
Lines after final 100. percent processed marker: **** SIMPLE_CTF_ESTIMATE NORMAL STOP **** **** Execution time: 48.8 seconds **** SIMPLE_DISTR_CTF_ESTIMATE NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 50.3 seconds Searched directory : /usr/local/data/actions-runner/SIMPLE_data_testing/SIMPLE_data_testing/SIMPLE_data_testing/motab/2_motion_correct Filter kind : mrc Found 100 file(s). Written to filetab.txt