SIMPLE Test Report - proteasome
SIMPLE test run
Execution times
1h 32m 47.4sTotal across 11 timed test steps
| Test step | Program | Duration |
|---|---|---|
| 11_refine3D_auto | refine3D_auto | 27m 38.4s1658.4 seconds |
| 10_abinitio3D | abinitio3D | 44m 14.1s2654.1 seconds |
| 9_abinitio3D_cavgs | abinitio3D_cavgs | 9m 11.3s551.3 seconds |
| 8_model_cavgs_rejection | model_cavgs_rejection | 1.9s1.9 seconds |
| 7_abinitio2D | abinitio2D | 4m 55.8s295.8 seconds |
| 6_extract | extract | 4.5s4.5 seconds |
| 5_pick | pick | 1m 04.1s64.1 seconds |
| 4_selection | selection | 0.2s0.2 seconds |
| 3_ctf_estimate | ctf_estimate | 22.7s22.7 seconds |
| 2_motion_correct | motion_correct | 4m 49.6s289.6 seconds |
| 1_import_movies | import_movies | 24.8s24.8 seconds |
Total is the sum of execution times recorded by SIMPLE in this test LOG.
11_refine3D_auto27m 38.4s
LOG summary: PROGRAM refine3D_auto
>>> % GREEDY SEARCHES 0.000 >>> DIST BTW BEST ORIS (DEG) AVG/SDEV/MIN/MAX: 2.322 6.752 0.023 150.598 >>> IN-PLANE DIST (DEG) AVG/SDEV/MIN/MAX: 1.670 5.824 0.000 139.909 >>> SHIFT INCR ARG AVG/SDEV/MIN/MAX: 0.169 0.174 0.000 4.800 >>> % SEARCH SPACE SCANNED AVG/SDEV/MIN/MAX: 100.000 0.000 100.000 100.000 >>> MATCHING LOW-PASS LIMIT AVG/SDEV/MIN/MAX: 4.967 0.000 4.967 4.967 >>> ESTIMATED LOW-PASS LIMIT AVG/SDEV/MIN/MAX: 0.000 0.000 0.000 0.000 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 6.279 0.000 6.279 6.279 >>> SCORE [0,1] AVG/SDEV/MIN/MAX: 0.375 0.002 0.369 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: no **** SIMPLE_REFINE3D NORMAL STOP **** >>> # SHARED-MEMORY THREADS USED BY rec3D MASTER PROCESS: 8 **** Execution time: 4.1 seconds **** Execution time: 4.5 seconds **** Execution time: 4.5 seconds **** Execution time: 4.6 seconds **** Execution time: 4.7 seconds **** Execution time: 4.7 seconds **** Execution time: 4.7 seconds **** Execution time: 4.8 seconds **** Execution time: 4.9 seconds **** Execution time: 4.9 seconds >>> FSC AREA SCORE / CONICAL FSC AREA RATIO (cFAR) STATE 1: 0.0718 >>> AUTOMASKING >>> FOUND: 33 CONNECTED COMPONENT(S) **** SIMPLE_VOLASSEMBLE NORMAL STOP **** **** SIMPLE_RECONSTRUCT3D NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 1658.4 seconds
10_abinitio3D44m 14.1s
orthogonal_reprojs_state01.jpg
LOG summary: PROGRAM abinitio3D
Recent FSC=0.143 resolution estimates: >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 7.396 0.000 7.396 7.396 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 7.396 0.000 7.396 7.396 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 7.396 0.000 7.396 7.396 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 7.396 0.000 7.396 7.396 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 7.564 0.000 7.564 7.564 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 7.396 0.000 7.396 7.396 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 7.396 0.000 7.396 7.396 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 7.396 0.000 7.396 7.396 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 7.396 0.000 7.396 7.396 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 7.396 0.000 7.396 7.396 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 7.396 0.000 7.396 7.396 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 7.396 0.000 7.396 7.396 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 7.396 0.000 7.396 7.396 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 7.564 0.000 7.564 7.564 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 7.396 0.000 7.396 7.396 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 7.564 0.000 7.564 7.564 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 7.564 0.000 7.564 7.564 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 7.235 0.000 7.235 7.235 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 7.396 0.000 7.396 7.396 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 7.396 0.000 7.396 7.396 Status: **** Execution time: 4.0 seconds **** Execution time: 4.5 seconds **** Execution time: 4.6 seconds **** Execution time: 4.6 seconds **** Execution time: 4.8 seconds **** Execution time: 4.8 seconds **** Execution time: 4.8 seconds **** Execution time: 5.0 seconds **** Execution time: 5.0 seconds **** Execution time: 5.1 seconds **** SIMPLE_VOLASSEMBLE NORMAL STOP **** **** SIMPLE_RECONSTRUCT3D NORMAL STOP **** **** SIMPLE_BOOTSTRAP_REC3D NORMAL STOP **** **** SIMPLE_ABINITIO3D NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 2654.1 seconds
9_abinitio3D_cavgs9m 11.3s
LOG summary: PROGRAM abinitio3D_cavgs
>>> >>> RE-PROJECTION OF THE FINAL VOLUME >>> >>> GENERATING PROJECTIONS **** SIMPLE_REPROJECT NORMAL STOP **** >>> SHIFTING IMAGES CLASS: 37 RANK: 1 CORR: 0.54 CLASS: 84 RANK: 2 CORR: 0.51 CLASS: 11 RANK: 3 CORR: 0.46 CLASS: 41 RANK: 4 CORR: 0.46 CLASS: 46 RANK: 5 CORR: 0.45 CLASS: 70 RANK: 6 CORR: 0.45 CLASS: 74 RANK: 7 CORR: 0.44 CLASS: 14 RANK: 8 CORR: 0.44 CLASS: 4 RANK: 9 CORR: 0.43 CLASS: 40 RANK: 10 CORR: 0.43 CLASS: 30 RANK: 11 CORR: 0.43 CLASS: 38 RANK: 12 CORR: 0.43 CLASS: 32 RANK: 13 CORR: 0.42 CLASS: 5 RANK: 14 CORR: 0.42 CLASS: 7 RANK: 15 CORR: 0.42 CLASS: 29 RANK: 16 CORR: 0.42 CLASS: 86 RANK: 17 CORR: 0.41 CLASS: 54 RANK: 18 CORR: 0.41 CLASS: 12 RANK: 19 CORR: 0.41 CLASS: 13 RANK: 20 CORR: 0.41 CLASS: 55 RANK: 21 CORR: 0.41 CLASS: 20 RANK: 22 CORR: 0.40 CLASS: 43 RANK: 23 CORR: 0.40 CLASS: 88 RANK: 24 CORR: 0.40 CLASS: 36 RANK: 25 CORR: 0.40 CLASS: 9 RANK: 26 CORR: 0.40 CLASS: 42 RANK: 27 CORR: 0.40 CLASS: 28 RANK: 28 CORR: 0.40 CLASS: 2 RANK: 29 CORR: 0.39 CLASS: 16 RANK: 30 CORR: 0.38 **** SIMPLE_RANK_CAVGS NORMAL STOP **** **** SIMPLE_ABINITIO3D_CAVGS NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 551.3 seconds
8_model_cavgs_rejection1.9s
LOG summary: PROGRAM model_cavgs_rejection
>>> PROGRAM: model_cavgs_rejection >>> EXECUTION DIRECTORY: 8_model_cavgs_rejection >>> CAVG QUALITY MODEL : chunk100mics >>> CAVG QUALITY CONTEXT : chunk >>> DEFAULT HARD GATES REJECTED: 38 >>> CAVG QUALITY SELECTED / REJECTED : 30 / 60 >>> 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: 30 >>> WROTE quality_rejected_cavgs.mrc #CAVGS: 60 >>> WROTE hard_gate_rejections.mrc #CAVGS: 38 >>> WROTE quality_ranked_cavgs.mrc #CAVGS: 90 >>> WROTE quality_ranked_cavgs.txt **** SIMPLE_MODEL_CAVGS_REJECTION NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 1.9 seconds
7_abinitio2D4m 55.8s
cavgs_iter027.jpg
LOG summary: PROGRAM abinitio2D
Final class ranking and status: CLASS: 46 RANK: 1 POP: 327 RES: 4.27 CLASS: 9 RANK: 2 POP: 415 RES: 4.32 CLASS: 40 RANK: 3 POP: 368 RES: 4.44 CLASS: 16 RANK: 4 POP: 475 RES: 4.44 CLASS: 20 RANK: 5 POP: 290 RES: 4.50 CLASS: 55 RANK: 6 POP: 316 RES: 4.62 CLASS: 2 RANK: 7 POP: 332 RES: 4.82 CLASS: 54 RANK: 8 POP: 296 RES: 5.84 CLASS: 29 RANK: 9 POP: 306 RES: 5.84 CLASS: 28 RANK: 10 POP: 352 RES: 5.94 CLASS: 88 RANK: 11 POP: 230 RES: 5.94 CLASS: 32 RANK: 12 POP: 317 RES: 6.05 CLASS: 43 RANK: 13 POP: 359 RES: 6.05 CLASS: 13 RANK: 14 POP: 348 RES: 6.05 CLASS: 36 RANK: 15 POP: 292 RES: 6.16 CLASS: 7 RANK: 16 POP: 303 RES: 6.66 CLASS: 12 RANK: 17 POP: 237 RES: 7.08 CLASS: 78 RANK: 18 POP: 190 RES: 7.40 CLASS: 42 RANK: 19 POP: 197 RES: 7.74 CLASS: 10 RANK: 20 POP: 138 RES: 8.12 CLASS: 67 RANK: 21 POP: 110 RES: 11.48 CLASS: 89 RANK: 22 POP: 92 RES: 11.89 CLASS: 80 RANK: 23 POP: 198 RES: 11.89 CLASS: 60 RANK: 24 POP: 76 RES: 11.89 CLASS: 65 RANK: 25 POP: 58 RES: 11.89 CLASS: 87 RANK: 26 POP: 72 RES: 12.80 CLASS: 26 RANK: 27 POP: 126 RES: 13.31 CLASS: 64 RANK: 28 POP: 109 RES: 13.31 CLASS: 86 RANK: 29 POP: 88 RES: 13.87 CLASS: 68 RANK: 30 POP: 68 RES: 14.47 CLASS: 33 RANK: 31 POP: 64 RES: 14.47 CLASS: 14 RANK: 32 POP: 152 RES: 15.13 CLASS: 18 RANK: 33 POP: 64 RES: 15.13 CLASS: 15 RANK: 34 POP: 81 RES: 15.13 CLASS: 90 RANK: 35 POP: 50 RES: 15.13 CLASS: 30 RANK: 36 POP: 91 RES: 15.85 CLASS: 11 RANK: 37 POP: 117 RES: 15.85 CLASS: 44 RANK: 38 POP: 63 RES: 15.85 CLASS: 45 RANK: 39 POP: 27 RES: 16.64 CLASS: 4 RANK: 40 POP: 126 RES: 16.64 CLASS: 50 RANK: 41 POP: 58 RES: 17.52 CLASS: 84 RANK: 42 POP: 99 RES: 18.49 CLASS: 76 RANK: 43 POP: 47 RES: 18.49 CLASS: 24 RANK: 44 POP: 48 RES: 18.49 CLASS: 8 RANK: 45 POP: 83 RES: 18.49 CLASS: 63 RANK: 46 POP: 65 RES: 19.58 CLASS: 58 RANK: 47 POP: 74 RES: 19.58 CLASS: 37 RANK: 48 POP: 83 RES: 19.58 CLASS: 62 RANK: 49 POP: 57 RES: 20.80 CLASS: 6 RANK: 50 POP: 47 RES: 20.80 CLASS: 48 RANK: 51 POP: 112 RES: 20.80 CLASS: 5 RANK: 52 POP: 114 RES: 20.80 CLASS: 38 RANK: 53 POP: 104 RES: 20.80 CLASS: 19 RANK: 54 POP: 79 RES: 20.80 CLASS: 73 RANK: 55 POP: 67 RES: 20.80 CLASS: 70 RANK: 56 POP: 121 RES: 20.80 CLASS: 59 RANK: 57 POP: 83 RES: 22.19 CLASS: 74 RANK: 58 POP: 132 RES: 22.19 CLASS: 47 RANK: 59 POP: 37 RES: 22.19 CLASS: 22 RANK: 60 POP: 24 RES: 22.19 CLASS: 41 RANK: 61 POP: 98 RES: 22.19 CLASS: 34 RANK: 62 POP: 40 RES: 22.19 CLASS: 3 RANK: 63 POP: 9 RES: 23.77 CLASS: 75 RANK: 64 POP: 40 RES: 23.77 CLASS: 85 RANK: 65 POP: 22 RES: 30.25 CLASS: 81 RANK: 66 POP: 48 RES: 30.25 CLASS: 72 RANK: 67 POP: 6 RES: 30.25 CLASS: 39 RANK: 68 POP: 29 RES: 33.28 CLASS: 69 RANK: 69 POP: 17 RES: 33.28 CLASS: 66 RANK: 70 POP: 21 RES: 33.28 CLASS: 31 RANK: 71 POP: 11 RES: 36.98 CLASS: 52 RANK: 72 POP: 17 RES: 36.98 CLASS: 49 RANK: 73 POP: 18 RES: 36.98 CLASS: 83 RANK: 74 POP: 8 RES: 36.98 CLASS: 61 RANK: 75 POP: 16 RES: 41.60 CLASS: 25 RANK: 76 POP: 6 RES: 41.60 CLASS: 23 RANK: 77 POP: 6 RES: 41.60 CLASS: 1 RANK: 78 POP: 22 RES: 47.54 CLASS: 21 RANK: 79 POP: 11 RES: 47.54 CLASS: 17 RANK: 80 POP: 9 RES: 47.54 CLASS: 57 RANK: 81 POP: 14 RES: 55.47 CLASS: 56 RANK: 82 POP: 9 RES: 55.47 CLASS: 27 RANK: 83 POP: 46 RES: 55.47 CLASS: 53 RANK: 84 POP: 4 RES: 55.47 CLASS: 79 RANK: 85 POP: 48 RES: 55.47 CLASS: 82 RANK: 86 POP: 5 RES: 66.56 CLASS: 71 RANK: 87 POP: 4 RES: 66.56 CLASS: 35 RANK: 88 POP: 40 RES: 83.20 CLASS: 77 RANK: 89 POP: 10 RES: 166.40 CLASS: 51 RANK: 90 POP: 2 RES: 331.50 Status: **** SIMPLE_MAKE_CAVGS NORMAL STOP **** **** Execution time: 3.6 seconds **** SIMPLE_MAKE_CAVGS NORMAL STOP **** **** Execution time: 3.7 seconds **** SIMPLE_MAKE_CAVGS NORMAL STOP **** **** Execution time: 3.9 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: 295.8 seconds
6_extract4.5s
LOG summary: PROGRAM extract
Lines after the last 100. percent of the micrographs processed: **** SIMPLE_EXTRACT NORMAL STOP **** **** Execution time: 2.3 seconds **** SIMPLE_EXTRACT NORMAL STOP **** **** Execution time: 2.3 seconds **** SIMPLE_EXTRACT_DISTR NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 4.5 seconds
5_pick1m 04.1s
LOG summary: PROGRAM pick
Lines after the last 100. percent of the micrographs processed: **** SIMPLE_PICK NORMAL STOP **** **** Execution time: 62.0 seconds **** SIMPLE_DISTR_PICK NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 64.1 seconds
4_selection0.2s
LOG summary: PROGRAM selection
Final class ranking and status: **** SELECTION NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 0.2 seconds
3_ctf_estimate22.7s
14sep05c_00024sq_00003hl_00002es.frames_ctf_estimate_diag.jpg
14sep05c_00024sq_00003hl_00005es.frames_ctf_estimate_diag.jpg
14sep05c_00024sq_00004hl_00002es.frames_ctf_estimate_diag.jpg
14sep05c_00024sq_00006hl_00003es.frames_ctf_estimate_diag.jpg
14sep05c_c_00003gr_00014sq_00002hl_00005es.frames_ctf_estimate_diag.jpg
14sep05c_c_00003gr_00014sq_00004hl_00004es.frames_ctf_estimate_diag.jpg
14sep05c_c_00003gr_00014sq_00005hl_00002es.frames_ctf_estimate_diag.jpg
14sep05c_c_00003gr_00014sq_00005hl_00003es.frames_ctf_estimate_diag.jpg
14sep05c_c_00003gr_00014sq_00005hl_00005es.frames_ctf_estimate_diag.jpg
14sep05c_c_00003gr_00014sq_00006hl_00002es.frames_ctf_estimate_diag.jpg
14sep05c_c_00003gr_00014sq_00006hl_00003es.frames_ctf_estimate_diag.jpg
14sep05c_c_00003gr_00014sq_00006hl_00005es.frames_ctf_estimate_diag.jpg
14sep05c_c_00003gr_00014sq_00007hl_00004es.frames_ctf_estimate_diag.jpg
14sep05c_c_00003gr_00014sq_00007hl_00005es.frames_ctf_estimate_diag.jpg
14sep05c_c_00003gr_00014sq_00008hl_00005es.frames_ctf_estimate_diag.jpg
14sep05c_c_00003gr_00014sq_00009hl_00004es.frames_ctf_estimate_diag.jpg
14sep05c_c_00003gr_00014sq_00010hl_00002es.frames_ctf_estimate_diag.jpg
14sep05c_c_00003gr_00014sq_00011hl_00002es.frames_ctf_estimate_diag.jpg
14sep05c_c_00003gr_00014sq_00011hl_00003es.frames_ctf_estimate_diag.jpg
14sep05c_c_00003gr_00014sq_00011hl_00004es.frames_ctf_estimate_diag.jpg
LOG summary: PROGRAM ctf_estimate
Lines after final 100. percent processed marker: **** SIMPLE_CTF_ESTIMATE NORMAL STOP **** **** Execution time: 20.4 seconds **** SIMPLE_DISTR_CTF_ESTIMATE NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 22.7 seconds
2_motion_correct4m 49.6s
14sep05c_00024sq_00003hl_00002es.frames_thumb.jpg
14sep05c_00024sq_00003hl_00005es.frames_thumb.jpg
14sep05c_00024sq_00004hl_00002es.frames_thumb.jpg
14sep05c_00024sq_00006hl_00003es.frames_thumb.jpg
14sep05c_c_00003gr_00014sq_00002hl_00005es.frames_thumb.jpg
14sep05c_c_00003gr_00014sq_00004hl_00004es.frames_thumb.jpg
14sep05c_c_00003gr_00014sq_00005hl_00002es.frames_thumb.jpg
14sep05c_c_00003gr_00014sq_00005hl_00003es.frames_thumb.jpg
14sep05c_c_00003gr_00014sq_00005hl_00005es.frames_thumb.jpg
14sep05c_c_00003gr_00014sq_00006hl_00002es.frames_thumb.jpg
14sep05c_c_00003gr_00014sq_00006hl_00003es.frames_thumb.jpg
14sep05c_c_00003gr_00014sq_00006hl_00005es.frames_thumb.jpg
14sep05c_c_00003gr_00014sq_00007hl_00004es.frames_thumb.jpg
14sep05c_c_00003gr_00014sq_00007hl_00005es.frames_thumb.jpg
14sep05c_c_00003gr_00014sq_00008hl_00005es.frames_thumb.jpg
14sep05c_c_00003gr_00014sq_00009hl_00004es.frames_thumb.jpg
14sep05c_c_00003gr_00014sq_00010hl_00002es.frames_thumb.jpg
14sep05c_c_00003gr_00014sq_00011hl_00002es.frames_thumb.jpg
14sep05c_c_00003gr_00014sq_00011hl_00003es.frames_thumb.jpg
14sep05c_c_00003gr_00014sq_00011hl_00004es.frames_thumb.jpg
LOG summary: PROGRAM motion_correct
Lines after final 100. percent processed marker: **** SIMPLE_MOTION_CORRECT NORMAL STOP **** **** Execution time: 283.3 seconds **** SIMPLE_DISTR_MOTION_CORRECT NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 289.6 seconds
1_import_movies24.8s
LOG summary: PROGRAM import_movies
>>> IMPORTED 20 MOVIE(S) >>> TOTAL NUMBER OF MOVIE(S): 20 **** IMPORT_MOVIES NORMAL STOP **** **** SIMPLE Git Commit: a7ca03a6 **** Execution time: 24.8 seconds