SIMPLE Test Report - betagal
SIMPLE test run
Execution times
1h 23m 43.1sTotal across 10 timed test steps
| Test step | Program | Duration |
|---|---|---|
| 10_refine3D_auto | refine3D_auto | 51m 59.8s3119.8 seconds |
| 9_abinitio3D | abinitio3D | 16m 03.1s963.1 seconds |
| 8_abinitio3D_cavgs | abinitio3D_cavgs | 9m 34.9s574.9 seconds |
| 7_model_cavgs_rejection | model_cavgs_rejection | 1.8s1.8 seconds |
| 6_abinitio2D | abinitio2D | 3m 25.3s205.3 seconds |
| 5_extract | extract | 3.5s3.5 seconds |
| 4_pick | pick | 33.3s33.3 seconds |
| 3_ctf_estimate | ctf_estimate | 18.1s18.1 seconds |
| 2_motion_correct | motion_correct | 1m 24.8s84.8 seconds |
| 1_import_movies | import_movies | 18.5s18.5 seconds |
Total is the sum of execution times recorded by SIMPLE in this test LOG.
10_refine3D_auto51m 59.8s
LOG summary: PROGRAM refine3D_auto
>>> DIST BTW BEST ORIS (DEG) AVG/SDEV/MIN/MAX: 0.411 0.322 0.001 3.188 >>> IN-PLANE DIST (DEG) AVG/SDEV/MIN/MAX: 0.313 1.401 0.000 46.636 >>> SHIFT INCR ARG AVG/SDEV/MIN/MAX: 0.029 0.048 0.000 0.534 >>> % SEARCH SPACE SCANNED AVG/SDEV/MIN/MAX: 100.000 0.000 100.000 100.000 >>> MATCHING LOW-PASS LIMIT AVG/SDEV/MIN/MAX: 3.578 0.000 3.578 3.578 >>> ESTIMATED LOW-PASS LIMIT AVG/SDEV/MIN/MAX: 0.000 0.000 0.000 0.000 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 3.263 0.000 3.263 3.263 >>> SCORE [0,1] AVG/SDEV/MIN/MAX: 0.380 0.005 0.366 0.390 >>> -------------------- 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: yes **** SIMPLE_REFINE3D NORMAL STOP **** >>> # SHARED-MEMORY THREADS USED BY rec3D MASTER PROCESS: 8 **** Execution time: 4.8 seconds **** Execution time: 5.1 seconds **** Execution time: 5.2 seconds **** Execution time: 5.3 seconds **** Execution time: 5.5 seconds **** Execution time: 5.6 seconds **** Execution time: 5.7 seconds **** Execution time: 5.7 seconds **** Execution time: 5.7 seconds **** Execution time: 5.8 seconds >>> FSC AREA SCORE / CONICAL FSC AREA RATIO (cFAR) STATE 1: 0.6427 >>> AUTOMASKING >>> FOUND: 1 CONNECTED COMPONENT(S) **** SIMPLE_VOLASSEMBLE NORMAL STOP **** >>> B-FACTOR DETERMINED TO: -57.43 **** SIMPLE_RECONSTRUCT3D NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 3119.8 seconds
9_abinitio3D16m 03.1s
orthogonal_reprojs_state01.jpg
LOG summary: PROGRAM abinitio3D
Recent FSC=0.143 resolution estimates: >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 5.042 0.000 5.042 5.042 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 5.042 0.000 5.042 5.042 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 5.042 0.000 5.042 5.042 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 5.042 0.000 5.042 5.042 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 5.042 0.000 5.042 5.042 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 4.622 0.000 4.622 4.622 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 4.622 0.000 4.622 4.622 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 4.622 0.000 4.622 4.622 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 4.622 0.000 4.622 4.622 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 4.622 0.000 4.622 4.622 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 4.622 0.000 4.622 4.622 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 4.622 0.000 4.622 4.622 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 4.160 0.000 4.160 4.160 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 4.160 0.000 4.160 4.160 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 4.160 0.000 4.160 4.160 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 4.160 0.000 4.160 4.160 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 4.160 0.000 4.160 4.160 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 4.010 0.000 4.010 4.010 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 3.962 0.000 3.962 3.962 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 3.962 0.000 3.962 3.962 Status: **** Execution time: 4.7 seconds **** Execution time: 5.2 seconds **** Execution time: 5.3 seconds **** Execution time: 5.4 seconds **** Execution time: 5.5 seconds **** Execution time: 5.5 seconds **** Execution time: 5.5 seconds **** Execution time: 5.6 seconds **** Execution time: 5.6 seconds **** Execution time: 5.7 seconds **** SIMPLE_VOLASSEMBLE NORMAL STOP **** **** SIMPLE_RECONSTRUCT3D NORMAL STOP **** **** SIMPLE_BOOTSTRAP_REC3D NORMAL STOP **** **** SIMPLE_ABINITIO3D NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 963.1 seconds
8_abinitio3D_cavgs9m 34.9s
LOG summary: PROGRAM abinitio3D_cavgs
CLASS: 42 RANK: 5 CORR: 0.61 CLASS: 44 RANK: 6 CORR: 0.61 CLASS: 85 RANK: 7 CORR: 0.61 CLASS: 58 RANK: 8 CORR: 0.60 CLASS: 38 RANK: 9 CORR: 0.60 CLASS: 76 RANK: 10 CORR: 0.60 CLASS: 66 RANK: 11 CORR: 0.60 CLASS: 23 RANK: 12 CORR: 0.60 CLASS: 8 RANK: 13 CORR: 0.60 CLASS: 6 RANK: 14 CORR: 0.60 CLASS: 64 RANK: 15 CORR: 0.59 CLASS: 9 RANK: 16 CORR: 0.59 CLASS: 11 RANK: 17 CORR: 0.59 CLASS: 34 RANK: 18 CORR: 0.58 CLASS: 57 RANK: 19 CORR: 0.58 CLASS: 19 RANK: 20 CORR: 0.58 CLASS: 25 RANK: 21 CORR: 0.58 CLASS: 30 RANK: 22 CORR: 0.58 CLASS: 73 RANK: 23 CORR: 0.58 CLASS: 62 RANK: 24 CORR: 0.56 CLASS: 53 RANK: 25 CORR: 0.55 CLASS: 75 RANK: 26 CORR: 0.55 CLASS: 84 RANK: 27 CORR: 0.55 CLASS: 54 RANK: 28 CORR: 0.54 CLASS: 71 RANK: 29 CORR: 0.53 CLASS: 81 RANK: 30 CORR: 0.52 CLASS: 86 RANK: 31 CORR: 0.47 CLASS: 20 RANK: 32 CORR: 0.42 CLASS: 1 RANK: 33 CORR: 0.37 CLASS: 5 RANK: 34 CORR: 0.36 CLASS: 87 RANK: 35 CORR: 0.36 CLASS: 31 RANK: 36 CORR: 0.35 CLASS: 60 RANK: 37 CORR: 0.30 CLASS: 16 RANK: 38 CORR: 0.29 CLASS: 12 RANK: 39 CORR: 0.23 CLASS: 13 RANK: 40 CORR: 0.23 **** SIMPLE_RANK_CAVGS NORMAL STOP **** **** SIMPLE_ABINITIO3D_CAVGS NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 574.9 seconds
7_model_cavgs_rejection1.8s
LOG summary: PROGRAM model_cavgs_rejection
>>> PROGRAM: model_cavgs_rejection >>> EXECUTION DIRECTORY: 7_model_cavgs_rejection >>> CAVG QUALITY MODEL : chunk100mics >>> CAVG QUALITY CONTEXT : chunk >>> DEFAULT HARD GATES REJECTED: 40 >>> CAVG QUALITY SELECTED / REJECTED : 40 / 50 >>> 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: 40 >>> WROTE quality_rejected_cavgs.mrc #CAVGS: 50 >>> WROTE hard_gate_rejections.mrc #CAVGS: 40 >>> WROTE quality_ranked_cavgs.mrc #CAVGS: 90 >>> WROTE quality_ranked_cavgs.txt **** SIMPLE_MODEL_CAVGS_REJECTION NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 1.8 seconds
6_abinitio2D3m 25.3s
cavgs_iter027.jpg
LOG summary: PROGRAM abinitio2D
Final class ranking and status: CLASS: 54 RANK: 1 POP: 84 RES: 6.66 CLASS: 84 RANK: 2 POP: 99 RES: 7.08 CLASS: 53 RANK: 3 POP: 91 RES: 7.23 CLASS: 30 RANK: 4 POP: 102 RES: 7.23 CLASS: 42 RANK: 5 POP: 116 RES: 7.23 CLASS: 19 RANK: 6 POP: 86 RES: 7.40 CLASS: 11 RANK: 7 POP: 106 RES: 7.56 CLASS: 85 RANK: 8 POP: 102 RES: 7.56 CLASS: 34 RANK: 9 POP: 108 RES: 7.56 CLASS: 76 RANK: 10 POP: 111 RES: 7.74 CLASS: 9 RANK: 11 POP: 113 RES: 7.74 CLASS: 38 RANK: 12 POP: 128 RES: 7.74 CLASS: 23 RANK: 13 POP: 95 RES: 7.92 CLASS: 73 RANK: 14 POP: 120 RES: 7.92 CLASS: 57 RANK: 15 POP: 103 RES: 8.12 CLASS: 58 RANK: 16 POP: 95 RES: 8.12 CLASS: 44 RANK: 17 POP: 99 RES: 8.12 CLASS: 62 RANK: 18 POP: 113 RES: 8.53 CLASS: 66 RANK: 19 POP: 83 RES: 8.76 CLASS: 63 RANK: 20 POP: 86 RES: 8.76 CLASS: 71 RANK: 21 POP: 104 RES: 8.76 CLASS: 50 RANK: 22 POP: 90 RES: 8.99 CLASS: 6 RANK: 23 POP: 92 RES: 9.24 CLASS: 25 RANK: 24 POP: 131 RES: 12.33 CLASS: 8 RANK: 25 POP: 82 RES: 15.13 CLASS: 81 RANK: 26 POP: 128 RES: 16.64 CLASS: 20 RANK: 27 POP: 44 RES: 16.64 CLASS: 64 RANK: 28 POP: 71 RES: 16.64 CLASS: 2 RANK: 29 POP: 99 RES: 16.64 CLASS: 31 RANK: 30 POP: 52 RES: 18.49 CLASS: 39 RANK: 31 POP: 68 RES: 18.49 CLASS: 15 RANK: 32 POP: 53 RES: 19.58 CLASS: 86 RANK: 33 POP: 61 RES: 19.58 CLASS: 75 RANK: 34 POP: 76 RES: 19.58 CLASS: 48 RANK: 35 POP: 51 RES: 20.80 CLASS: 87 RANK: 36 POP: 66 RES: 20.80 CLASS: 37 RANK: 37 POP: 6 RES: 20.80 CLASS: 45 RANK: 38 POP: 38 RES: 22.19 CLASS: 7 RANK: 39 POP: 43 RES: 23.77 CLASS: 59 RANK: 40 POP: 21 RES: 23.77 CLASS: 72 RANK: 41 POP: 47 RES: 23.77 CLASS: 5 RANK: 42 POP: 28 RES: 25.60 CLASS: 16 RANK: 43 POP: 23 RES: 25.60 CLASS: 4 RANK: 44 POP: 56 RES: 25.60 CLASS: 14 RANK: 45 POP: 59 RES: 27.73 CLASS: 12 RANK: 46 POP: 18 RES: 27.73 CLASS: 40 RANK: 47 POP: 11 RES: 27.73 CLASS: 1 RANK: 48 POP: 56 RES: 27.73 CLASS: 55 RANK: 49 POP: 29 RES: 30.25 CLASS: 18 RANK: 50 POP: 10 RES: 30.25 CLASS: 13 RANK: 51 POP: 19 RES: 33.28 CLASS: 52 RANK: 52 POP: 12 RES: 33.28 CLASS: 26 RANK: 53 POP: 46 RES: 33.28 CLASS: 43 RANK: 54 POP: 8 RES: 33.28 CLASS: 60 RANK: 55 POP: 28 RES: 36.98 CLASS: 74 RANK: 56 POP: 37 RES: 36.98 CLASS: 68 RANK: 57 POP: 7 RES: 36.98 CLASS: 51 RANK: 58 POP: 24 RES: 41.60 CLASS: 90 RANK: 59 POP: 37 RES: 41.60 CLASS: 82 RANK: 60 POP: 14 RES: 41.60 CLASS: 35 RANK: 61 POP: 23 RES: 41.60 CLASS: 17 RANK: 62 POP: 50 RES: 41.60 CLASS: 67 RANK: 63 POP: 17 RES: 41.60 CLASS: 56 RANK: 64 POP: 27 RES: 47.54 CLASS: 49 RANK: 65 POP: 21 RES: 47.54 CLASS: 22 RANK: 66 POP: 7 RES: 47.54 CLASS: 70 RANK: 67 POP: 24 RES: 47.54 CLASS: 69 RANK: 68 POP: 4 RES: 47.54 CLASS: 32 RANK: 69 POP: 24 RES: 47.54 CLASS: 3 RANK: 70 POP: 8 RES: 55.47 CLASS: 29 RANK: 71 POP: 34 RES: 55.47 CLASS: 27 RANK: 72 POP: 10 RES: 55.47 CLASS: 24 RANK: 73 POP: 8 RES: 55.47 CLASS: 46 RANK: 74 POP: 8 RES: 55.47 CLASS: 21 RANK: 75 POP: 9 RES: 55.47 CLASS: 83 RANK: 76 POP: 6 RES: 55.47 CLASS: 77 RANK: 77 POP: 11 RES: 55.47 CLASS: 47 RANK: 78 POP: 6 RES: 66.56 Status: **** SIMPLE_MAKE_CAVGS NORMAL STOP **** **** Execution time: 2.0 seconds **** SIMPLE_MAKE_CAVGS NORMAL STOP **** **** Execution time: 2.0 seconds **** SIMPLE_MAKE_CAVGS NORMAL STOP **** **** Execution time: 2.1 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: 205.3 seconds
5_extract3.5s
LOG summary: PROGRAM extract
Lines after the last 100. percent of the micrographs processed: **** SIMPLE_EXTRACT NORMAL STOP **** **** Execution time: 1.5 seconds **** SIMPLE_EXTRACT NORMAL STOP **** **** Execution time: 1.6 seconds **** SIMPLE_EXTRACT NORMAL STOP **** **** Execution time: 1.6 seconds **** SIMPLE_EXTRACT_DISTR NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 3.5 seconds
4_pick33.3s
LOG summary: PROGRAM pick
Lines after the last 100. percent of the micrographs processed: **** SIMPLE_PICK NORMAL STOP **** **** Execution time: 31.4 seconds **** SIMPLE_DISTR_PICK NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 33.3 seconds
3_ctf_estimate18.1s
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LOG summary: PROGRAM ctf_estimate
Lines after final 100. percent processed marker: **** SIMPLE_CTF_ESTIMATE NORMAL STOP **** **** Execution time: 16.0 seconds **** SIMPLE_DISTR_CTF_ESTIMATE NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 18.1 seconds Searched directory : /usr/local/data/actions-runner/SIMPLE_data_testing/SIMPLE_data_testing/SIMPLE_data_testing/betagal/2_motion_correct Filter kind : mrc Found 24 file(s). Written to filetab.txt
2_motion_correct1m 24.8s
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LOG summary: PROGRAM motion_correct
Lines after final 100. percent processed marker: **** SIMPLE_MOTION_CORRECT NORMAL STOP **** **** Execution time: 82.7 seconds **** SIMPLE_DISTR_MOTION_CORRECT NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 84.8 seconds
1_import_movies18.5s
LOG summary: PROGRAM import_movies
>>> IMPORTED 24 MOVIE(S) >>> TOTAL NUMBER OF MOVIE(S): 24 **** IMPORT_MOVIES NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 18.5 seconds