SIMPLE test run
| Test step | Program | Duration |
|---|---|---|
| 11_refine3D_auto | refine3D_auto | 27m 33.4s1653.4 seconds |
| 10_abinitio3D | abinitio3D | 17m 30.7s1050.7 seconds |
| 9_abinitio3D_cavgs | abinitio3D_cavgs | 8m 54.0s534.0 seconds |
| 8_model_cavgs_rejection | model_cavgs_rejection | 1.4s1.4 seconds |
| 7_abinitio2D | abinitio2D | 3m 01.4s181.4 seconds |
| 6_extract | extract | 3.6s3.6 seconds |
| 5_pick | pick | 55.3s55.3 seconds |
| 4_selection | selection | 0.2s0.2 seconds |
| 3_ctf_estimate | ctf_estimate | 28.4s28.4 seconds |
| 2_motion_correct | motion_correct | 6m 44.3s404.3 seconds |
| 1_import_movies | import_movies | 9.5s9.5 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: 1.222 2.909 0.000 70.472 >>> IN-PLANE DIST (DEG) AVG/SDEV/MIN/MAX: 0.698 3.021 0.000 94.091 >>> SHIFT INCR ARG AVG/SDEV/MIN/MAX: 0.149 0.177 0.000 1.112 >>> % 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: 11.886 0.000 11.886 11.886 >>> SCORE [0,1] AVG/SDEV/MIN/MAX: 0.373 0.002 0.369 0.380 >>> -------------------- 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: 1.8 seconds **** Execution time: 1.9 seconds **** Execution time: 2.0 seconds **** Execution time: 2.0 seconds **** Execution time: 2.1 seconds **** Execution time: 2.1 seconds **** Execution time: 2.1 seconds **** Execution time: 2.2 seconds **** Execution time: 2.2 seconds **** Execution time: 2.2 seconds >>> FSC AREA SCORE / CONICAL FSC AREA RATIO (cFAR) STATE 1: 0.3753 >>> AUTOMASKING >>> FOUND: 220 CONNECTED COMPONENT(S) **** SIMPLE_VOLASSEMBLE NORMAL STOP **** **** SIMPLE_RECONSTRUCT3D NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 1653.4 seconds
Recent FSC=0.143 resolution estimates: >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 16.640 0.000 16.640 16.640 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 15.848 0.000 15.848 15.848 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 15.127 0.000 15.127 15.127 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 13.312 0.000 13.312 13.312 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 13.312 0.000 13.312 13.312 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 13.312 0.000 13.312 13.312 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 13.312 0.000 13.312 13.312 >>> 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: 12.326 0.000 12.326 12.326 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 12.326 0.000 12.326 12.326 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 12.326 0.000 12.326 12.326 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 12.326 0.000 12.326 12.326 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 12.326 0.000 12.326 12.326 Status: **** Execution time: 1.6 seconds **** Execution time: 1.7 seconds **** Execution time: 1.9 seconds **** Execution time: 2.1 seconds **** Execution time: 2.1 seconds **** Execution time: 2.1 seconds **** Execution time: 2.1 seconds **** Execution time: 2.1 seconds **** Execution time: 2.1 seconds **** Execution time: 2.1 seconds **** SIMPLE_VOLASSEMBLE NORMAL STOP **** **** SIMPLE_RECONSTRUCT3D NORMAL STOP **** **** SIMPLE_BOOTSTRAP_REC3D NORMAL STOP **** **** SIMPLE_ABINITIO3D NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 1050.7 seconds
>>> FSC AREA SCORE / CONICAL FSC AREA RATIO (cFAR) STATE 1: 0.0246 **** SIMPLE_VOLASSEMBLE NORMAL STOP **** **** SIMPLE_RECONSTRUCT3D NORMAL STOP **** >>> BOOTSTRAP_REC3D SIGMA SCALE STATE 1: 10.000 >>> 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: 0.0231 **** 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: 25 RANK: 1 CORR: 0.37 CLASS: 42 RANK: 2 CORR: 0.37 CLASS: 21 RANK: 3 CORR: 0.37 CLASS: 28 RANK: 4 CORR: 0.37 CLASS: 52 RANK: 5 CORR: 0.37 CLASS: 84 RANK: 6 CORR: 0.37 CLASS: 26 RANK: 7 CORR: 0.36 CLASS: 6 RANK: 8 CORR: 0.36 CLASS: 61 RANK: 9 CORR: 0.36 CLASS: 22 RANK: 10 CORR: 0.36 CLASS: 74 RANK: 11 CORR: 0.36 CLASS: 1 RANK: 12 CORR: 0.36 CLASS: 13 RANK: 13 CORR: 0.35 CLASS: 71 RANK: 14 CORR: 0.35 CLASS: 78 RANK: 15 CORR: 0.35 CLASS: 4 RANK: 16 CORR: 0.34 CLASS: 2 RANK: 17 CORR: 0.33 CLASS: 20 RANK: 18 CORR: 0.32 CLASS: 11 RANK: 19 CORR: 0.32 CLASS: 59 RANK: 20 CORR: 0.30 **** SIMPLE_RANK_CAVGS NORMAL STOP **** **** SIMPLE_ABINITIO3D_CAVGS NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 534.0 seconds
>>> PROGRAM: model_cavgs_rejection >>> EXECUTION DIRECTORY: 8_model_cavgs_rejection >>> CAVG QUALITY MODEL : chunk100mics >>> CAVG QUALITY CONTEXT : chunk >>> DEFAULT HARD GATES REJECTED: 68 >>> CAVG QUALITY SELECTED / REJECTED : 20 / 70 >>> 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: 20 >>> WROTE quality_rejected_cavgs.mrc #CAVGS: 70 >>> WROTE hard_gate_rejections.mrc #CAVGS: 68 >>> WROTE quality_ranked_cavgs.mrc #CAVGS: 90 >>> WROTE quality_ranked_cavgs.txt **** SIMPLE_MODEL_CAVGS_REJECTION NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 1.4 seconds
Final class ranking and status: CLASS: 22 RANK: 1 POP: 57 RES: 15.13 CLASS: 26 RANK: 2 POP: 81 RES: 16.64 CLASS: 78 RANK: 3 POP: 81 RES: 16.64 CLASS: 71 RANK: 4 POP: 45 RES: 16.64 CLASS: 42 RANK: 5 POP: 86 RES: 17.52 CLASS: 25 RANK: 6 POP: 88 RES: 17.52 CLASS: 6 RANK: 7 POP: 51 RES: 17.52 CLASS: 48 RANK: 8 POP: 116 RES: 19.58 CLASS: 37 RANK: 9 POP: 5 RES: 20.80 CLASS: 74 RANK: 10 POP: 70 RES: 20.80 CLASS: 62 RANK: 11 POP: 64 RES: 22.19 CLASS: 30 RANK: 12 POP: 26 RES: 22.19 CLASS: 11 RANK: 13 POP: 53 RES: 22.19 CLASS: 21 RANK: 14 POP: 59 RES: 22.19 CLASS: 59 RANK: 15 POP: 48 RES: 22.19 CLASS: 23 RANK: 16 POP: 29 RES: 23.77 CLASS: 34 RANK: 17 POP: 4 RES: 23.77 CLASS: 52 RANK: 18 POP: 89 RES: 23.77 CLASS: 13 RANK: 19 POP: 48 RES: 23.77 CLASS: 82 RANK: 20 POP: 8 RES: 23.77 CLASS: 41 RANK: 21 POP: 19 RES: 23.77 CLASS: 2 RANK: 22 POP: 54 RES: 23.77 CLASS: 12 RANK: 23 POP: 17 RES: 25.60 CLASS: 28 RANK: 24 POP: 54 RES: 25.60 CLASS: 84 RANK: 25 POP: 45 RES: 25.60 CLASS: 1 RANK: 26 POP: 50 RES: 25.60 CLASS: 61 RANK: 27 POP: 56 RES: 25.60 CLASS: 20 RANK: 28 POP: 38 RES: 30.25 CLASS: 7 RANK: 29 POP: 64 RES: 33.28 CLASS: 4 RANK: 30 POP: 17 RES: 33.28 CLASS: 46 RANK: 31 POP: 16 RES: 36.98 CLASS: 66 RANK: 32 POP: 109 RES: 36.98 CLASS: 8 RANK: 33 POP: 12 RES: 36.98 CLASS: 57 RANK: 34 POP: 12 RES: 41.60 CLASS: 39 RANK: 35 POP: 6 RES: 41.60 CLASS: 54 RANK: 36 POP: 89 RES: 41.60 CLASS: 5 RANK: 37 POP: 74 RES: 41.60 CLASS: 70 RANK: 38 POP: 79 RES: 41.60 CLASS: 58 RANK: 39 POP: 15 RES: 47.54 CLASS: 88 RANK: 40 POP: 11 RES: 47.54 CLASS: 83 RANK: 41 POP: 149 RES: 47.54 CLASS: 72 RANK: 42 POP: 6 RES: 47.54 CLASS: 44 RANK: 43 POP: 48 RES: 47.54 CLASS: 73 RANK: 44 POP: 13 RES: 47.54 CLASS: 81 RANK: 45 POP: 5 RES: 55.47 CLASS: 14 RANK: 46 POP: 8 RES: 55.47 CLASS: 56 RANK: 47 POP: 91 RES: 55.47 CLASS: 27 RANK: 48 POP: 46 RES: 55.47 CLASS: 53 RANK: 49 POP: 79 RES: 55.47 CLASS: 3 RANK: 50 POP: 4 RES: 55.47 CLASS: 50 RANK: 51 POP: 81 RES: 55.47 CLASS: 49 RANK: 52 POP: 14 RES: 55.47 CLASS: 45 RANK: 53 POP: 110 RES: 55.47 CLASS: 86 RANK: 54 POP: 22 RES: 55.47 CLASS: 40 RANK: 55 POP: 106 RES: 55.47 CLASS: 43 RANK: 56 POP: 122 RES: 55.47 CLASS: 9 RANK: 57 POP: 118 RES: 55.47 CLASS: 68 RANK: 58 POP: 10 RES: 55.47 CLASS: 63 RANK: 59 POP: 13 RES: 66.56 CLASS: 15 RANK: 60 POP: 72 RES: 66.56 CLASS: 24 RANK: 61 POP: 28 RES: 66.56 CLASS: 47 RANK: 62 POP: 73 RES: 66.56 CLASS: 90 RANK: 63 POP: 13 RES: 66.56 CLASS: 80 RANK: 64 POP: 93 RES: 66.56 CLASS: 77 RANK: 65 POP: 25 RES: 66.56 CLASS: 35 RANK: 66 POP: 66 RES: 66.56 CLASS: 69 RANK: 67 POP: 9 RES: 66.56 CLASS: 67 RANK: 68 POP: 101 RES: 66.56 CLASS: 16 RANK: 69 POP: 84 RES: 66.56 CLASS: 29 RANK: 70 POP: 9 RES: 83.20 CLASS: 55 RANK: 71 POP: 65 RES: 83.20 CLASS: 10 RANK: 72 POP: 96 RES: 83.20 CLASS: 38 RANK: 73 POP: 90 RES: 83.20 CLASS: 32 RANK: 74 POP: 11 RES: 83.20 CLASS: 60 RANK: 75 POP: 86 RES: 110.93 CLASS: 89 RANK: 76 POP: 79 RES: 110.93 CLASS: 19 RANK: 77 POP: 73 RES: 110.93 CLASS: 18 RANK: 78 POP: 73 RES: 166.40 Status: **** SIMPLE_MAKE_CAVGS NORMAL STOP **** **** Execution time: 2.3 seconds **** SIMPLE_MAKE_CAVGS NORMAL STOP **** **** Execution time: 2.3 seconds **** SIMPLE_MAKE_CAVGS NORMAL STOP **** **** Execution time: 2.4 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: 181.4 seconds
Lines after the last 100. percent of the micrographs processed: **** SIMPLE_EXTRACT NORMAL STOP **** **** Execution time: 1.6 seconds **** SIMPLE_EXTRACT NORMAL STOP **** **** Execution time: 1.7 seconds **** SIMPLE_EXTRACT NORMAL STOP **** **** Execution time: 1.7 seconds **** SIMPLE_EXTRACT_DISTR NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 3.6 seconds
Lines after the last 100. percent of the micrographs processed: **** SIMPLE_PICK NORMAL STOP **** **** Execution time: 53.8 seconds **** SIMPLE_DISTR_PICK NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 55.3 seconds
Final class ranking and status: **** SELECTION NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 0.2 seconds
Lines after final 100. percent processed marker: **** SIMPLE_CTF_ESTIMATE NORMAL STOP **** **** Execution time: 26.5 seconds **** SIMPLE_DISTR_CTF_ESTIMATE NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 28.4 seconds Searched directory : /usr/local/data/actions-runner/SIMPLE_data_testing/SIMPLE_data_testing/SIMPLE_data_testing/trpm4/2_motion_correct Filter kind : mrc Found 50 file(s). Written to filetab.txt