SIMPLE test run
| Test step | Program | Duration |
|---|---|---|
| 11_refine3D_auto | refine3D_auto | 45m 22.2s2722.2 seconds |
| 10_abinitio3D | abinitio3D | 23m 00.1s1380.1 seconds |
| 9_abinitio3D_cavgs | abinitio3D_cavgs | 8m 59.8s539.8 seconds |
| 8_model_cavgs_rejection | model_cavgs_rejection | 2.4s2.4 seconds |
| 7_abinitio2D | abinitio2D | 4m 42.1s282.1 seconds |
| 6_extract | extract | 5.4s5.4 seconds |
| 5_pick | pick | 1m 04.7s64.7 seconds |
| 4_selection | selection | 0.1s0.1 seconds |
| 3_ctf_estimate | ctf_estimate | 13.3s13.3 seconds |
| 2_motion_correct | motion_correct | 4m 53.5s293.5 seconds |
| 1_import_movies | import_movies | 33.3s33.3 seconds |
Total is the sum of execution times recorded by SIMPLE in this test LOG.
>>> % SEARCH SPACE SCANNED AVG/SDEV/MIN/MAX: 100.000 0.000 100.000 100.000 >>> MATCHING LOW-PASS LIMIT (THIS ITERATION) 3.200 >>> NU HANDOFF LP (NEXT) AVG/SDEV/MIN/MAX: 3.200 0.000 3.200 3.200 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 3.200 0.000 3.200 3.200 >>> RESOLUTION @ FSC=0.5 AVG/SDEV/MIN/MAX: 3.739 0.000 3.739 3.739 >>> SCORE [0,1] AVG/SDEV/MIN/MAX: 0.381 0.004 0.372 0.392 >>> -------------------- 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_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 31.1 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: 0.7115 **** SIMPLE_VOLASSEMBLE NORMAL STOP **** >>> POSTPROCESS: FSC from fsc_state01.bin, 0.5/0.143 at 3.74/ 3.20 A >>> B-FACTOR (UNFILTERED PAIR) DETERMINED TO: -105.24 >>> POSTPROCESS: B -105.24 capped at the cutoff shell: gain 13.06 from shell 104 to Nyquist >>> 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 3.20 A **** SIMPLE_RECONSTRUCT3D NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 2722.2 seconds
Recent FSC=0.143 resolution estimates: >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 5.547 0.000 5.547 5.547 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 5.547 0.000 5.547 5.547 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 5.547 0.000 5.547 5.547 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 5.547 0.000 5.547 5.547 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 5.547 0.000 5.547 5.547 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 5.547 0.000 5.547 5.547 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 5.547 0.000 5.547 5.547 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 5.547 0.000 5.547 5.547 >>> 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: 4.160 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: 3.962 0.000 3.962 3.962 >>> 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: **** 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: 1380.1 seconds
CLASS: 68 RANK: 3 CORR: 0.76 CLASS: 39 RANK: 4 CORR: 0.76 CLASS: 78 RANK: 5 CORR: 0.76 CLASS: 53 RANK: 6 CORR: 0.75 CLASS: 80 RANK: 7 CORR: 0.75 CLASS: 2 RANK: 8 CORR: 0.75 CLASS: 10 RANK: 9 CORR: 0.75 CLASS: 66 RANK: 10 CORR: 0.74 CLASS: 4 RANK: 11 CORR: 0.74 CLASS: 46 RANK: 12 CORR: 0.74 CLASS: 87 RANK: 13 CORR: 0.74 CLASS: 84 RANK: 14 CORR: 0.74 CLASS: 62 RANK: 15 CORR: 0.73 CLASS: 70 RANK: 16 CORR: 0.73 CLASS: 57 RANK: 17 CORR: 0.73 CLASS: 38 RANK: 18 CORR: 0.73 CLASS: 8 RANK: 19 CORR: 0.72 CLASS: 22 RANK: 20 CORR: 0.68 CLASS: 34 RANK: 21 CORR: 0.68 CLASS: 81 RANK: 22 CORR: 0.67 CLASS: 64 RANK: 23 CORR: 0.65 CLASS: 41 RANK: 24 CORR: 0.65 CLASS: 74 RANK: 25 CORR: 0.61 CLASS: 69 RANK: 26 CORR: 0.59 CLASS: 48 RANK: 27 CORR: 0.58 CLASS: 26 RANK: 28 CORR: 0.56 CLASS: 49 RANK: 29 CORR: 0.52 CLASS: 29 RANK: 30 CORR: 0.51 CLASS: 23 RANK: 31 CORR: 0.50 CLASS: 50 RANK: 32 CORR: 0.50 CLASS: 24 RANK: 33 CORR: 0.50 CLASS: 19 RANK: 34 CORR: 0.48 CLASS: 86 RANK: 35 CORR: 0.47 CLASS: 42 RANK: 36 CORR: 0.46 CLASS: 83 RANK: 37 CORR: 0.46 CLASS: 15 RANK: 38 CORR: 0.46 **** SIMPLE_RANK_CAVGS NORMAL STOP **** **** SIMPLE_ABINITIO3D_CAVGS NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 539.8 seconds
>>> PROGRAM: model_cavgs_rejection >>> EXECUTION DIRECTORY: 8_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: 38 >>> CAVG QUALITY SELECTED / REJECTED : 38 / 52 >>> 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: 38 >>> WROTE quality_rejected_cavgs.mrc #CAVGS: 52 >>> 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: 3cad71a1 **** Execution time: 2.4 seconds
Final class ranking and status: CLASS: 39 RANK: 1 POP: 455 RES: 3.78 CLASS: 62 RANK: 2 POP: 422 RES: 3.92 CLASS: 53 RANK: 3 POP: 349 RES: 3.96 CLASS: 84 RANK: 4 POP: 316 RES: 4.06 CLASS: 66 RANK: 5 POP: 270 RES: 4.11 CLASS: 87 RANK: 6 POP: 341 RES: 4.11 CLASS: 80 RANK: 7 POP: 511 RES: 4.21 CLASS: 4 RANK: 8 POP: 429 RES: 4.21 CLASS: 70 RANK: 9 POP: 318 RES: 4.21 CLASS: 8 RANK: 10 POP: 417 RES: 4.27 CLASS: 38 RANK: 11 POP: 294 RES: 4.38 CLASS: 22 RANK: 12 POP: 232 RES: 5.46 CLASS: 2 RANK: 13 POP: 266 RES: 5.64 CLASS: 68 RANK: 14 POP: 319 RES: 5.84 CLASS: 46 RANK: 15 POP: 248 RES: 5.84 CLASS: 41 RANK: 16 POP: 264 RES: 6.93 CLASS: 81 RANK: 17 POP: 201 RES: 6.93 CLASS: 50 RANK: 18 POP: 153 RES: 7.08 CLASS: 42 RANK: 19 POP: 200 RES: 7.23 CLASS: 15 RANK: 20 POP: 229 RES: 7.40 CLASS: 83 RANK: 21 POP: 150 RES: 7.92 CLASS: 44 RANK: 22 POP: 182 RES: 7.92 CLASS: 13 RANK: 23 POP: 161 RES: 8.53 CLASS: 35 RANK: 24 POP: 135 RES: 8.99 CLASS: 54 RANK: 25 POP: 70 RES: 10.74 CLASS: 78 RANK: 26 POP: 138 RES: 11.89 CLASS: 3 RANK: 27 POP: 103 RES: 13.31 CLASS: 58 RANK: 28 POP: 114 RES: 13.87 CLASS: 48 RANK: 29 POP: 114 RES: 13.87 CLASS: 89 RANK: 30 POP: 22 RES: 13.87 CLASS: 7 RANK: 31 POP: 74 RES: 13.87 CLASS: 86 RANK: 32 POP: 163 RES: 17.52 CLASS: 74 RANK: 33 POP: 121 RES: 17.52 CLASS: 34 RANK: 34 POP: 80 RES: 18.49 CLASS: 29 RANK: 35 POP: 131 RES: 18.49 CLASS: 49 RANK: 36 POP: 136 RES: 18.49 CLASS: 21 RANK: 37 POP: 74 RES: 18.49 CLASS: 71 RANK: 38 POP: 25 RES: 18.49 CLASS: 17 RANK: 39 POP: 74 RES: 18.49 CLASS: 75 RANK: 40 POP: 62 RES: 19.58 CLASS: 31 RANK: 41 POP: 11 RES: 20.80 CLASS: 19 RANK: 42 POP: 173 RES: 20.80 CLASS: 24 RANK: 43 POP: 121 RES: 20.80 CLASS: 79 RANK: 44 POP: 43 RES: 20.80 CLASS: 69 RANK: 45 POP: 116 RES: 20.80 CLASS: 64 RANK: 46 POP: 92 RES: 20.80 CLASS: 30 RANK: 47 POP: 47 RES: 22.19 CLASS: 57 RANK: 48 POP: 42 RES: 22.19 CLASS: 26 RANK: 49 POP: 161 RES: 22.19 CLASS: 12 RANK: 50 POP: 107 RES: 22.19 CLASS: 23 RANK: 51 POP: 141 RES: 22.19 CLASS: 90 RANK: 52 POP: 37 RES: 22.19 CLASS: 45 RANK: 53 POP: 41 RES: 22.19 CLASS: 10 RANK: 54 POP: 49 RES: 22.19 CLASS: 72 RANK: 55 POP: 52 RES: 22.19 CLASS: 65 RANK: 56 POP: 47 RES: 22.19 CLASS: 60 RANK: 57 POP: 54 RES: 23.77 CLASS: 67 RANK: 58 POP: 70 RES: 23.77 CLASS: 37 RANK: 59 POP: 29 RES: 25.60 CLASS: 5 RANK: 60 POP: 7 RES: 27.73 CLASS: 88 RANK: 61 POP: 43 RES: 30.25 CLASS: 77 RANK: 62 POP: 33 RES: 30.25 CLASS: 16 RANK: 63 POP: 44 RES: 30.25 CLASS: 32 RANK: 64 POP: 18 RES: 30.25 CLASS: 51 RANK: 65 POP: 18 RES: 33.28 CLASS: 76 RANK: 66 POP: 26 RES: 33.28 CLASS: 63 RANK: 67 POP: 15 RES: 36.98 CLASS: 59 RANK: 68 POP: 28 RES: 36.98 CLASS: 28 RANK: 69 POP: 24 RES: 36.98 CLASS: 6 RANK: 70 POP: 17 RES: 36.98 CLASS: 25 RANK: 71 POP: 17 RES: 36.98 CLASS: 18 RANK: 72 POP: 20 RES: 36.98 CLASS: 9 RANK: 73 POP: 11 RES: 36.98 CLASS: 56 RANK: 74 POP: 8 RES: 41.60 CLASS: 73 RANK: 75 POP: 14 RES: 41.60 CLASS: 55 RANK: 76 POP: 38 RES: 47.54 CLASS: 85 RANK: 77 POP: 5 RES: 47.54 CLASS: 14 RANK: 78 POP: 49 RES: 55.47 CLASS: 40 RANK: 79 POP: 8 RES: 55.47 CLASS: 36 RANK: 80 POP: 5 RES: 55.47 CLASS: 61 RANK: 81 POP: 9 RES: 66.56 CLASS: 1 RANK: 82 POP: 33 RES: 66.56 CLASS: 27 RANK: 83 POP: 15 RES: 166.40 CLASS: 33 RANK: 84 POP: 4 RES: 166.40 CLASS: 52 RANK: 85 POP: 2 RES: 332.80 CLASS: 11 RANK: 86 POP: 2 RES: 332.80 CLASS: 20 RANK: 87 POP: 3 RES: 332.80 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: 282.1 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: 5.4 seconds
100. percent micrographs marker not found; recent pick diagnostics: >>> PICK: 5 PART(S) COMPLETED IN 64.0 s **** SIMPLE_DISTR_PICK NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 64.7 seconds
Final class ranking and status: **** SELECTION NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 0.1 seconds
100. percent marker not found; recent CTF diagnostics: >>> CTF_ESTIMATE: 16 PART(S) COMPLETED IN 13.0 s **** SIMPLE_DISTR_CTF_ESTIMATE NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 13.3 seconds
100. percent marker not found; recent motion-correction diagnostics: **** SIMPLE_DISTR_MOTION_CORRECT NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 293.5 seconds
>>> IMPORTED 20 MOVIE(S) >>> TOTAL NUMBER OF MOVIE(S): 20 **** IMPORT_MOVIES NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 33.3 seconds