SIMPLE Test Report - betagal
SIMPLE test run
Execution times
53m 13.2sTotal across 10 timed test steps
| Test step | Program | Duration |
|---|---|---|
| 10_refine3D_auto | refine3D_auto | 22m 42.7s1362.7 seconds |
| 9_abinitio3D | abinitio3D | 15m 53.2s953.2 seconds |
| 8_abinitio3D_cavgs | abinitio3D_cavgs | 8m 44.6s524.6 seconds |
| 7_model_cavgs_rejection | model_cavgs_rejection | 2.4s2.4 seconds |
| 6_abinitio2D | abinitio2D | 3m 15.2s195.2 seconds |
| 5_extract | extract | 3.2s3.2 seconds |
| 4_pick | pick | 20.6s20.6 seconds |
| 3_ctf_estimate | ctf_estimate | 14.4s14.4 seconds |
| 2_motion_correct | motion_correct | 1m 36.9s96.9 seconds |
| 1_import_movies | import_movies | 20.0s20.0 seconds |
Total is the sum of execution times recorded by SIMPLE in this test LOG.
10_refine3D_auto22m 42.7s
orientations_distribution_state01.jpg
orthogonal_reprojs_state01.jpg
LOG summary: PROGRAM refine3D_auto
>>> % SEARCH SPACE SCANNED AVG/SDEV/MIN/MAX: 100.000 0.000 100.000 100.000 >>> MATCHING LOW-PASS LIMIT (THIS ITERATION) 3.362 >>> NU HANDOFF LP (NEXT) AVG/SDEV/MIN/MAX: 3.362 0.000 3.362 3.362 >>> RESOLUTION @ FSC=0.143 AVG/SDEV/MIN/MAX: 3.362 0.000 3.362 3.362 >>> RESOLUTION @ FSC=0.5 AVG/SDEV/MIN/MAX: 3.915 0.000 3.915 3.915 >>> SCORE [0,1] AVG/SDEV/MIN/MAX: 0.390 0.006 0.374 0.405 >>> -------------------- 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 8.0 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: 0.6255 **** SIMPLE_VOLASSEMBLE NORMAL STOP **** >>> POSTPROCESS: FSC from fsc_state01.bin, 0.5/0.143 at 3.92/ 3.36 A >>> B-FACTOR (UNFILTERED PAIR) DETERMINED TO: -58.13 >>> POSTPROCESS: B -58.13 capped at the cutoff shell: gain 3.62 from shell 99 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 3.36 A **** SIMPLE_RECONSTRUCT3D NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 1362.7 seconds
9_abinitio3D15m 53.2s
orientations_distribution_state01.jpg
orientations_distribution_state01_stage04.jpg
orientations_distribution_state01_stage05.jpg
orientations_distribution_state01_stage06.jpg
orientations_distribution_state01_stage07.jpg
orientations_distribution_state01_stage08.jpg
orthogonal_reprojs_state01.jpg
orthogonal_reprojs_state01_stage04.jpg
orthogonal_reprojs_state01_stage05.jpg
orthogonal_reprojs_state01_stage06.jpg
orthogonal_reprojs_state01_stage07.jpg
orthogonal_reprojs_state01_stage08.jpg
LOG summary: PROGRAM abinitio3D
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: 5.042 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: 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: 4.160 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: 953.2 seconds
8_abinitio3D_cavgs8m 44.6s
orientations_distribution_state01.jpg
LOG summary: PROGRAM abinitio3D_cavgs
CLASS: 86 RANK: 3 CORR: 0.95 CLASS: 27 RANK: 4 CORR: 0.94 CLASS: 28 RANK: 5 CORR: 0.93 CLASS: 89 RANK: 6 CORR: 0.93 CLASS: 24 RANK: 7 CORR: 0.93 CLASS: 15 RANK: 8 CORR: 0.91 CLASS: 25 RANK: 9 CORR: 0.90 CLASS: 48 RANK: 10 CORR: 0.90 CLASS: 59 RANK: 11 CORR: 0.89 CLASS: 22 RANK: 12 CORR: 0.88 CLASS: 68 RANK: 13 CORR: 0.87 CLASS: 2 RANK: 14 CORR: 0.85 CLASS: 56 RANK: 15 CORR: 0.84 CLASS: 39 RANK: 16 CORR: 0.82 CLASS: 63 RANK: 17 CORR: 0.80 CLASS: 84 RANK: 18 CORR: 0.77 CLASS: 57 RANK: 19 CORR: 0.75 CLASS: 16 RANK: 20 CORR: 0.75 CLASS: 18 RANK: 21 CORR: 0.71 CLASS: 4 RANK: 22 CORR: 0.70 CLASS: 76 RANK: 23 CORR: 0.70 CLASS: 52 RANK: 24 CORR: 0.65 CLASS: 37 RANK: 25 CORR: 0.64 CLASS: 33 RANK: 26 CORR: 0.64 CLASS: 21 RANK: 27 CORR: 0.64 CLASS: 34 RANK: 28 CORR: 0.64 CLASS: 8 RANK: 29 CORR: 0.64 CLASS: 74 RANK: 30 CORR: 0.63 CLASS: 45 RANK: 31 CORR: 0.62 CLASS: 71 RANK: 32 CORR: 0.59 CLASS: 65 RANK: 33 CORR: 0.57 CLASS: 6 RANK: 34 CORR: 0.56 CLASS: 29 RANK: 35 CORR: 0.53 CLASS: 23 RANK: 36 CORR: 0.49 CLASS: 11 RANK: 37 CORR: 0.47 CLASS: 69 RANK: 38 CORR: 0.47 **** SIMPLE_RANK_CAVGS NORMAL STOP **** **** SIMPLE_ABINITIO3D_CAVGS NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 524.6 seconds
7_model_cavgs_rejection2.4s
LOG summary: PROGRAM model_cavgs_rejection
>>> PROGRAM: model_cavgs_rejection >>> EXECUTION DIRECTORY: 7_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: 40 >>> 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: 40 >>> 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
6_abinitio2D3m 15.2s
cavgs_iter027.jpg
LOG summary: PROGRAM abinitio2D
Final class ranking and status: CLASS: 4 RANK: 1 POP: 106 RES: 6.40 CLASS: 27 RANK: 2 POP: 94 RES: 6.40 CLASS: 57 RANK: 3 POP: 162 RES: 6.79 CLASS: 84 RANK: 4 POP: 91 RES: 7.08 CLASS: 74 RANK: 5 POP: 142 RES: 7.40 CLASS: 68 RANK: 6 POP: 105 RES: 7.40 CLASS: 63 RANK: 7 POP: 112 RES: 7.56 CLASS: 59 RANK: 8 POP: 110 RES: 7.56 CLASS: 86 RANK: 9 POP: 96 RES: 7.74 CLASS: 56 RANK: 10 POP: 138 RES: 7.74 CLASS: 76 RANK: 11 POP: 110 RES: 7.92 CLASS: 22 RANK: 12 POP: 131 RES: 8.12 CLASS: 53 RANK: 13 POP: 125 RES: 8.32 CLASS: 89 RANK: 14 POP: 111 RES: 8.32 CLASS: 33 RANK: 15 POP: 136 RES: 8.76 CLASS: 34 RANK: 16 POP: 83 RES: 8.99 CLASS: 48 RANK: 17 POP: 104 RES: 8.99 CLASS: 24 RANK: 18 POP: 99 RES: 8.99 CLASS: 37 RANK: 19 POP: 102 RES: 9.51 CLASS: 21 RANK: 20 POP: 94 RES: 9.51 CLASS: 23 RANK: 21 POP: 15 RES: 9.51 CLASS: 52 RANK: 22 POP: 137 RES: 10.08 CLASS: 2 RANK: 23 POP: 85 RES: 11.09 CLASS: 8 RANK: 24 POP: 94 RES: 11.89 CLASS: 25 RANK: 25 POP: 61 RES: 12.33 CLASS: 82 RANK: 26 POP: 118 RES: 15.85 CLASS: 65 RANK: 27 POP: 115 RES: 16.64 CLASS: 11 RANK: 28 POP: 34 RES: 16.64 CLASS: 41 RANK: 29 POP: 60 RES: 18.49 CLASS: 88 RANK: 30 POP: 6 RES: 18.49 CLASS: 39 RANK: 31 POP: 63 RES: 18.49 CLASS: 71 RANK: 32 POP: 122 RES: 18.49 CLASS: 28 RANK: 33 POP: 59 RES: 19.58 CLASS: 1 RANK: 34 POP: 49 RES: 19.58 CLASS: 45 RANK: 35 POP: 56 RES: 20.80 CLASS: 14 RANK: 36 POP: 50 RES: 23.77 CLASS: 79 RANK: 37 POP: 15 RES: 25.60 CLASS: 6 RANK: 38 POP: 42 RES: 25.60 CLASS: 18 RANK: 39 POP: 29 RES: 25.60 CLASS: 69 RANK: 40 POP: 48 RES: 25.60 CLASS: 15 RANK: 41 POP: 18 RES: 27.73 CLASS: 72 RANK: 42 POP: 18 RES: 27.73 CLASS: 81 RANK: 43 POP: 19 RES: 27.73 CLASS: 32 RANK: 44 POP: 48 RES: 27.73 CLASS: 26 RANK: 45 POP: 12 RES: 30.25 CLASS: 49 RANK: 46 POP: 52 RES: 30.25 CLASS: 46 RANK: 47 POP: 47 RES: 30.25 CLASS: 20 RANK: 48 POP: 14 RES: 30.25 CLASS: 40 RANK: 49 POP: 47 RES: 30.25 CLASS: 16 RANK: 50 POP: 27 RES: 30.25 CLASS: 7 RANK: 51 POP: 22 RES: 33.28 CLASS: 51 RANK: 52 POP: 7 RES: 33.28 CLASS: 3 RANK: 53 POP: 27 RES: 33.28 CLASS: 43 RANK: 54 POP: 31 RES: 33.28 CLASS: 64 RANK: 55 POP: 27 RES: 33.28 CLASS: 60 RANK: 56 POP: 57 RES: 36.98 CLASS: 29 RANK: 57 POP: 25 RES: 36.98 CLASS: 17 RANK: 58 POP: 22 RES: 36.98 CLASS: 58 RANK: 59 POP: 19 RES: 41.60 CLASS: 80 RANK: 60 POP: 6 RES: 41.60 CLASS: 78 RANK: 61 POP: 37 RES: 41.60 CLASS: 9 RANK: 62 POP: 12 RES: 41.60 CLASS: 61 RANK: 63 POP: 12 RES: 47.54 CLASS: 55 RANK: 64 POP: 11 RES: 47.54 CLASS: 13 RANK: 65 POP: 17 RES: 47.54 CLASS: 90 RANK: 66 POP: 11 RES: 47.54 CLASS: 87 RANK: 67 POP: 8 RES: 47.54 CLASS: 42 RANK: 68 POP: 6 RES: 47.54 CLASS: 77 RANK: 69 POP: 11 RES: 47.54 CLASS: 73 RANK: 70 POP: 13 RES: 47.54 CLASS: 47 RANK: 71 POP: 15 RES: 55.47 CLASS: 70 RANK: 72 POP: 15 RES: 55.47 CLASS: 31 RANK: 73 POP: 6 RES: 66.56 CLASS: 66 RANK: 74 POP: 8 RES: 66.56 CLASS: 5 RANK: 75 POP: 2 RES: 332.80 CLASS: 67 RANK: 76 POP: 2 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: 195.2 seconds
5_extract3.2s
ptcls_sample.jpg
ptcls_sample_lp.jpg
LOG summary: PROGRAM extract
100. percent micrographs marker not found; recent extract diagnostics: >>> EXTRACT: 24 PART(S) COMPLETED IN 2.0 s **** SIMPLE_EXTRACT_DISTR NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 3.2 seconds
4_pick20.6s
LOG summary: PROGRAM pick
100. percent micrographs marker not found; recent pick diagnostics: >>> PICK: 24 PART(S) COMPLETED IN 20.0 s **** SIMPLE_DISTR_PICK NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 20.6 seconds
3_ctf_estimate14.4s
20170629_00021_frameImage_ctf_estimate_diag.jpg
20170629_00022_frameImage_ctf_estimate_diag.jpg
20170629_00023_frameImage_ctf_estimate_diag.jpg
20170629_00024_frameImage_ctf_estimate_diag.jpg
20170629_00025_frameImage_ctf_estimate_diag.jpg
20170629_00026_frameImage_ctf_estimate_diag.jpg
20170629_00027_frameImage_ctf_estimate_diag.jpg
20170629_00028_frameImage_ctf_estimate_diag.jpg
20170629_00029_frameImage_ctf_estimate_diag.jpg
20170629_00030_frameImage_ctf_estimate_diag.jpg
20170629_00031_frameImage_ctf_estimate_diag.jpg
20170629_00035_frameImage_ctf_estimate_diag.jpg
20170629_00036_frameImage_ctf_estimate_diag.jpg
20170629_00037_frameImage_ctf_estimate_diag.jpg
20170629_00039_frameImage_ctf_estimate_diag.jpg
20170629_00040_frameImage_ctf_estimate_diag.jpg
20170629_00042_frameImage_ctf_estimate_diag.jpg
20170629_00043_frameImage_ctf_estimate_diag.jpg
20170629_00044_frameImage_ctf_estimate_diag.jpg
20170629_00045_frameImage_ctf_estimate_diag.jpg
20170629_00046_frameImage_ctf_estimate_diag.jpg
20170629_00047_frameImage_ctf_estimate_diag.jpg
20170629_00048_frameImage_ctf_estimate_diag.jpg
20170629_00049_frameImage_ctf_estimate_diag.jpg
LOG summary: PROGRAM ctf_estimate
100. percent marker not found; recent CTF diagnostics: >>> CTF_ESTIMATE: 24 PART(S) COMPLETED IN 14.0 s **** SIMPLE_DISTR_CTF_ESTIMATE NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 14.4 seconds
2_motion_correct1m 36.9s
20170629_00021_frameImage_thumb.jpg
20170629_00022_frameImage_thumb.jpg
20170629_00023_frameImage_thumb.jpg
20170629_00024_frameImage_thumb.jpg
20170629_00025_frameImage_thumb.jpg
20170629_00026_frameImage_thumb.jpg
20170629_00027_frameImage_thumb.jpg
20170629_00028_frameImage_thumb.jpg
20170629_00029_frameImage_thumb.jpg
20170629_00030_frameImage_thumb.jpg
20170629_00031_frameImage_thumb.jpg
20170629_00035_frameImage_thumb.jpg
20170629_00036_frameImage_thumb.jpg
20170629_00037_frameImage_thumb.jpg
20170629_00039_frameImage_thumb.jpg
20170629_00040_frameImage_thumb.jpg
20170629_00042_frameImage_thumb.jpg
20170629_00043_frameImage_thumb.jpg
20170629_00044_frameImage_thumb.jpg
20170629_00045_frameImage_thumb.jpg
20170629_00046_frameImage_thumb.jpg
20170629_00047_frameImage_thumb.jpg
20170629_00048_frameImage_thumb.jpg
20170629_00049_frameImage_thumb.jpg
gain_thumb.jpg
LOG summary: PROGRAM motion_correct
100. percent marker not found; recent motion-correction diagnostics: **** SIMPLE_DISTR_MOTION_CORRECT NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 96.9 seconds
1_import_movies20.0s
movthumb1.jpg
LOG summary: PROGRAM import_movies
>>> IMPORTED 24 MOVIE(S) >>> TOTAL NUMBER OF MOVIE(S): 24 **** IMPORT_MOVIES NORMAL STOP **** **** SIMPLE Git Commit: 3cad71a1 **** Execution time: 20.0 seconds