mqaprna.py ver: f69479e-dirty start 2018-04-04 19:53:08 -------------------------- ---------------------------------------------------- Seq ss fn /home/mqapRNA/mqapRNAweb/media/jobs/1eb3aa05-2e6a-48bd-96c1-3923d6bec032/ss.txt Output csv /home/mqapRNA/mqapRNAweb/media/jobs/1eb3aa05-2e6a-48bd-96c1-3923d6bec032/1eb3aa0_raw.csv Input files #5 ['input/1zzn_crystalstr_renum.pdb', 'input/1zzn-on-1x8w_ModeRNA.pdb', 'input/1zzn-on-1x8w_SimRNA_QRNA.pdb'] RNAkb 5pt Model path /home/magnus/Dropbox/WORK_/mqaprna-papier/SVMlin.rda Multiprocessing on Verbose off Ignore pdb fn off Methods ClashScore,AnalyzeGeometry,FARNA,SimRNA_0,RNAscore,eSCORE,RNAkb,SSAgreement,FARNA_hires,RASP,RNAkb_all rmsd biopython_all Native pdb off RASP all -------------------------- ---------------------------------------------------- AnalyzeGeometry on SSAgreement on pdb_id >seq ref_seq CAUAUGGCCGUGUGCCUUGCGCCGGGAAACCACGCAAGGGAUGGUGUCAAAUUCGGCGAAACCUAAGCGCCCGCCCGGGCGUAUGGCAACGCCGAGCCAAGCUUCGGCGCCUGCGCCGAUGAAGGUGUAGAGACUAGACGGCACCCACCUAAGGCAAACGCUAUGGUGAAGGCAUAGUCCAGGGAGUGGCGAAAGCCACACAAACCAGACGGCC ref_ss .....((((((.(((((((((..((....)).)))))))...((((((...(.((((....((...((((((....))))))..))....)))))(((.....((((((....))))))....))).............))))))((((...(((....)))..)))).................(((((....)))))......)).)))))) to ignore 0 [] files to analyze: 5 ['input/1zzn_crystalstr_renum.pdb', 'input/1zzn-on-1x8w_ModeRNA.pdb', 'input/1zzn-on-1x8w_SimRNA_QRNA.pdb', 'input/1zzn-on-1y0q_ModeRNA.pdb', 'input/1zzn-on-1y0q-SimRNA_QRNA.pdb'] -------------------------------------------------------------------------------- Wrong middle line: ATOM 4270 O RA A 190 23.275 0.582 -18.337 1.00 99.99 O O [---------------- ] 1 20.0 % 5 10 True 1zzn-on-1x8w_ModeRNA.pdb {'AnalyzeGeometry': 0.0, 'eSCORE': 2.4339, 'FARNA': ['-6.814', '-25.647', '-9.756', '-14.475', '-7.55', '-85.74', '191.284', '1422.404', '-62.437', '1445.366', '0.0', '0.0', '44.097', '0.0'], 'ClashScore': 152.818129, 'length': 214, 'SimRNA_0': ['0', '63.138952', '180.205', '-68.001', '350.344', '-467.410075', '-104.022', '61.468', '-92.942', '-38.419', '-293.494', '', '63.138952'], 'FARNA_hires': ['0.0', '428.354', '-4.911', '0.0', '17.662', '84.005', '-17.373', '55.548', '-331.884', '18.468', '-229.437', '335.569', '-8.57', '464.444', '44.833'], 'RNAscore': nan, 'RASP': ['48.1561', '2957', '0.0162855', '67.5945', '9.02686', '-2.1534', '-14223.4', '182167', '-0.0780789', '-13402.9', '90.4052', '-9.0758', '-30705.3', '414283', '-0.0741167', '-28727.3', '190.275', '-10.3956', '-54835.5', '1409327', '-0.038909', '0', '0', '0'], 'RNAkb': ['7.81837e+04', '2.35849e+04', '2.07898e+04', '2.72691e+01', '0.00000e+00', '0.00000e+00', '5.55152e-03', '0.00000e+00', '1.22586e+05', '4.61352e-09', '1.22586e+05'], 'RNAkb_all': ['7.81837e+04', '2.35849e+04', '2.07898e+04', '2.72691e+01', '0.00000e+00', '0.00000e+00', '-1.84424e-03', '0.00000e+00', '1.22586e+05', '4.61352e-09', '1.22586e+05'], 'SSAgreement': 'error'} [-------------------------------- ] 2 40.0 % 5 10 True 1zzn-on-1y0q-SimRNA_QRNA.pdb {'AnalyzeGeometry': 0.0, 'eSCORE': 4.00485, 'FARNA': ['-85.216', '-48.571', '-68.212', '-300.283', '-57.505', '-740.373', '242.179', '121.333', '-112.322', '-1020.109', '0.0', '0.0', '28.861', '0.0'], 'ClashScore': 30.491329, 'length': 214, 'SimRNA_0': ['0', '-1447.411601', '-696.258', '-158.570', '2.564', '-753.717632', '-120.423', '-93.456', '-120.814', '-63.063', '-355.962', '', '-1447.411601'], 'FARNA_hires': ['0.0', '-1116.112', '-2.904', '0.0', '5.476', '79.878', '-1110.421', '42.1', '-581.908', '13.285', '-333.014', '125.887', '-29.358', '641.084', '33.784'], 'RNAscore': nan, 'RASP': ['-7.1282', '3199', '-0.00222826', '35.2924', '7.24835', '-5.85245', '-17634.2', '199739', '-0.0882861', '-16307.8', '101.562', '-13.0595', '-39798.3', '453338', '-0.0877895', '-35843.7', '190.208', '-20.7907', '-89314.9', '1533941', '-0.0582258', '0', '0', '0'], 'RNAkb': -1, 'RNAkb_all': -1, 'SSAgreement': 'error'} [------------------------------------------------ ] 3 60.0 % 5 10 True 1zzn-on-1x8w_SimRNA_QRNA.pdb {'AnalyzeGeometry': 0.0, 'eSCORE': 4.11782, 'FARNA': ['-84.424', '-49.063', '-56.125', '-302.036', '-46.586', '-738.655', '205.315', '99.774', '-81.937', '-1024.422', '0.0', '0.0', '29.314', '0.0'], 'ClashScore': 42.943898, 'length': 214, 'SimRNA_0': ['0', '-1441.466809', '-706.055', '-188.324', '0.856', '-736.268482', '-126.283', '-125.291', '-105.453', '-52.579', '-326.663', '', '-1441.466809'], 'FARNA_hires': ['0.0', '-1103.336', '-4.874', '0.0', '6.612', '59.742', '-1058.93', '40.771', '-579.331', '8.158', '-315.217', '91.404', '-34.174', '616.793', '65.709'], 'RNAscore': nan, 'RASP': ['1.7512', '3204', '0.000546567', '37.6472', '7.26146', '-4.94336', '-16127.6', '198054', '-0.0814302', '-14818.2', '102.133', '-12.8203', '-36714.7', '449095', '-0.0817526', '-32726.5', '182.407', '-21.8643', '-84452.1', '1526237', '-0.0553335', '0', '0', '0'], 'RNAkb': -1, 'RNAkb_all': -1, 'SSAgreement': 'error'} Wrong middle line: ATOM 4270 O RA A 190 23.275 0.582 -18.337 1.00 99.99 O O [---------------------------------------------------------------- ] 4 80.0 % 5 10 True 1zzn_crystalstr_renum.pdb {'AnalyzeGeometry': 0.0, 'eSCORE': 3.98531, 'FARNA': ['-85.863', '-65.022', '-65.376', '-280.714', '-52.962', '-792.917', '217.358', '61.824', '-110.995', '-1144.092', '0.0', '0.0', '30.575', '0.0'], 'ClashScore': 58.26596, 'length': 214, 'SimRNA_0': 'error', 'FARNA_hires': ['0.0', '-1475.498', '-2.011', '0.0', '5.701', '25.135', '-1342.338', '41.789', '-642.024', '11.416', '-341.397', '83.719', '-29.914', '695.074', '19.352'], 'RNAscore': 26.0457, 'RASP': ['-28.1007', '3314', '-0.00847939', '24.5979', '6.66684', '-7.90459', '-19311.4', '205187', '-0.094116', '-17785', '94.3432', '-16.1786', '-43028.6', '468162', '-0.0919096', '-38597.3', '182.237', '-24.3163', '-94975.1', '1578330', '-0.0601744', '0', '0', '0'], 'RNAkb': -1, 'RNAkb_all': -1, 'SSAgreement': 'error'} [--------------------------------------------------------------------------------] 5 100.0 % 5 10 True 1zzn-on-1y0q_ModeRNA.pdb {'AnalyzeGeometry': 0.0, 'eSCORE': 3.07103, 'FARNA': ['-66.198', '-55.954', '-59.316', '-192.569', '-51.784', '-625.984', '262.445', '632.178', '-125.728', '-253.475', '0.0', '0.0', '29.434', '0.0'], 'ClashScore': 125.054466, 'length': 214, 'SimRNA_0': ['0', '-444.920308', '15.414', '-87.819', '166.970', '-627.304100', '-122.060', '-56.486', '-95.613', '-53.224', '-299.921', '', '-444.920308'], 'FARNA_hires': ['0.0', '-844.124', '-1.99', '0.0', '7.65', '29.734', '-623.133', '56.586', '-518.743', '15.024', '-338.005', '99.757', '-95.224', '492.854', '31.367'], 'RNAscore': nan, 'RASP': ['21.4962', '3280', '0.00655372', '57.2332', '7.75972', '-4.60545', '-15610.7', '204303', '-0.0764096', '-14493.5', '101.499', '-11.0073', '-34992.5', '465023', '-0.075249', '-31551.7', '186.335', '-18.4657', '-68044.8', '1569052', '-0.0433668', '0', '0', '0'], 'RNAkb': ['4.10473e+04', '2.22775e+04', '2.02848e+04', '1.23297e+01', '0.00000e+00', '0.00000e+00', '2.65083e-03', '0.00000e+00', '8.36219e+04', '3.78032e-09', '8.36219e+04'], 'RNAkb_all': ['4.10473e+04', '2.22775e+04', '2.02848e+04', '1.23297e+01', '0.00000e+00', '0.00000e+00', '-1.69079e-03', '0.00000e+00', '8.36219e+04', '3.78032e-09', '8.36219e+04'], 'SSAgreement': 'error'} Cmd: mqaprna.py -s /home/mqapRNA/mqapRNAweb/media/jobs/1eb3aa05-2e6a-48bd-96c1-3923d6bec032/ss.txt -m 6 -f -o /home/mqapRNA/mqapRNAweb/media/jobs/1eb3aa05-2e6a-48bd-96c1-3923d6bec032/1eb3aa0_raw.csv input/1zzn_crystalstr_renum.pdb input/1zzn-on-1x8w_ModeRNA.pdb input/1zzn-on-1x8w_SimRNA_QRNA.pdb input/1zzn-on-1y0q_ModeRNA.pdb input/1zzn-on-1y0q-SimRNA_QRNA.pdb Execution time: 0:33:58.434 process: 6 start: 19:53:08 end: 20:27:07 Output: /home/mqapRNA/mqapRNAweb/media/jobs/1eb3aa05-2e6a-48bd-96c1-3923d6bec032/1eb3aa0_raw.csv logging: /home/mqapRNA/mqapRNAweb/media/jobs/1eb3aa05-2e6a-48bd-96c1-3923d6bec032/1eb3aa0_raw.log logging wrappers /home/mqapRNA/mqaprna_env/log/ in: /home/mqapRNA/mqapRNAweb/media/jobs/1eb3aa05-2e6a-48bd-96c1-3923d6bec032/1eb3aa0_raw.csv model_key: grid-8a6dfea4-1f6e-4354-9396-f727a5bd937a_model_14 Checking whether there is an H2O instance running at http://localhost:54321. connected. Warning: Your H2O cluster version is too old (11 months and 16 days)! Please download and install the latest version from http://h2o.ai/download/ -------------------------- ------------------------- H2O cluster uptime: 55 days 6 hours 21 mins H2O cluster version: 3.10.4.5 H2O cluster version age: 11 months and 16 days !!! H2O cluster name: magnus H2O cluster total nodes: 1 H2O cluster free memory: 828 Mb H2O cluster total cores: 8 H2O cluster allowed cores: 8 H2O cluster status: locked, healthy H2O connection url: http://localhost:54321 H2O connection proxy: H2O internal security: False Python version: 2.7.6 final -------------------------- ------------------------- Parse progress: [#########################################################] 100% fn clash_score analyze_geometry farna_rna_base_axis farna_rna_backbone_backbone farna_rna_base_stack_axis farna_rna_base_stagger farna_rna_base_stack farna_rna_base_pair farna_rna_repulsive farna_rna_vdw farna_rna_base_backbone farna_score_lowres farna_rna_data_backbone farna_linear_chainbreak farna_rna_rg farna_atom_pair_constraint simrna_steps simrna_total_energy simrna_base_base simrna_short_stacking simrna_base_backbone simrna_local_geometry simrna_bonds_dist_cp simrna_bonds_dist_pc simrna_flat_angles_cpc simrna_flat_angles_pcp simrna_tors_eta_theta simrna_sphere_penalty simrna_chain_energy x3rnascore escore rnakb_bond rnakb_angle rnakb_proper_dih rnakb_improper_dih rnakb_lj14 rnakb_coulomb14 rnakb_lj_sr rnakb_coulomb_sr rnakb_potential rnakb_kinetic_en rnakb_total_energy ss_disagreement farna_atom_pair_constraint_hires farna_score_hires farna_hbond_sr_bb_sc farna_linear_chainbreak_hires farna_fa_intra_rep farna_rna_sugar_close farna_hbond_sc farna_lk_nonpolar farna_fa_atr farna_fa_elec_rna_phos_phos farna_ch_bond farna_fa_rep farna_hbond_lr_bb_sc farna_geom_sol farna_rna_torsion rasp_c3_pdb_energy rasp_c3_no_contacts rasp_c3_norm_energy rasp_c3_mean_energy rasp_c3_sd_energy rasp_c3_zscore rasp_bb_pdb_energy rasp_bb_no_contacts rasp_bb_norm_energy rasp_bb_mean_energy rasp_bb_sd_energy rasp_bb_zscore rasp_bbr_pdb_energy rasp_bbr_no_contacts rasp_bbr_norm_energy rasp_bbr_mean_energy rasp_bbr_sd_energy rasp_bbr_zscore rasp_all_pdb_energy rasp_all_no_contacts rasp_all_norm_energy rasp_all_mean_energy rasp_all_sd_energy rasp_all_zscore rnakb_bond_all rnakb_angle_all rnakb_proper_dih_all rnakb_improper_dih_all rnakb_lj14_all rnakb_coulomb14_all rnakb_lj_sr_all rnakb_coulomb_sr_all rnakb_potential_all rnakb_kinetic_en_all rnakb_total_energy_all ---------------------------- ------------- ------------------ --------------------- ----------------------------- --------------------------- ------------------------ ---------------------- --------------------- --------------------- --------------- ------------------------- -------------------- ------------------------- ------------------------- -------------- ---------------------------- -------------- --------------------- ------------------ ----------------------- ---------------------- ----------------------- ---------------------- ---------------------- ------------------------ ------------------------ ----------------------- ----------------------- --------------------- ------------ -------- ------------ ------------- ------------------ -------------------- ------------ 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---------------------- ------------------------ ---------------- --------------------- ----------------- ---------------------- --------------------- ---------------------- ------------------------ 1zzn-on-1x8w_ModeRNA.pdb 152.818 0 -6.814 -25.647 -9.756 -14.475 -7.55 -85.74 191.284 1422.4 -62.437 1445.37 0 0 44.097 0 0 63.139 180.205 -68.001 350.344 -467.41 -104.022 61.468 -92.942 -38.419 -293.494 nan 63.139 nan 2.4339 78183.7 23584.9 20789.8 27.2691 0 0 0.00555152 0 122586 4.61352e-09 122586 nan 0 428.354 -4.911 0 17.662 84.005 -17.373 55.548 -331.884 18.468 -229.437 335.569 -8.57 464.444 44.833 48.1561 2957 0.0162855 67.5945 9.02686 -2.1534 -14223.4 182167 -0.0780789 -13402.9 90.4052 -9.0758 -30705.3 414283 -0.0741167 -28727.3 190.275 -10.3956 -54835.5 1.40933e+06 -0.038909 0 0 0 78183.7 23584.9 20789.8 27.2691 0 0 -0.00184424 0 122586 4.61352e-09 122586 1zzn-on-1y0q-SimRNA_QRNA.pdb 30.4913 0 -85.216 -48.571 -68.212 -300.283 -57.505 -740.373 242.179 121.333 -112.322 -1020.11 0 0 28.861 0 0 -1447.41 -696.258 -158.57 2.564 -753.718 -120.423 -93.456 -120.814 -63.063 -355.962 nan -1447.41 nan 4.00485 -1 nan 0 -1116.11 -2.904 0 5.476 79.878 -1110.42 42.1 -581.908 13.285 -333.014 125.887 -29.358 641.084 33.784 -7.1282 3199 -0.00222826 35.2924 7.24835 -5.85245 -17634.2 199739 -0.0882861 -16307.8 101.562 -13.0595 -39798.3 453338 -0.0877895 -35843.7 190.208 -20.7907 -89314.9 1.53394e+06 -0.0582258 0 0 0 -1 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan 1zzn-on-1x8w_SimRNA_QRNA.pdb 42.9439 0 -84.424 -49.063 -56.125 -302.036 -46.586 -738.655 205.315 99.774 -81.937 -1024.42 0 0 29.314 0 0 -1441.47 -706.055 -188.324 0.856 -736.268 -126.283 -125.291 -105.453 -52.579 -326.663 nan -1441.47 nan 4.11782 -1 nan 0 -1103.34 -4.874 0 6.612 59.742 -1058.93 40.771 -579.331 8.158 -315.217 91.404 -34.174 616.793 65.709 1.7512 3204 0.000546567 37.6472 7.26146 -4.94336 -16127.6 198054 -0.0814302 -14818.2 102.133 -12.8203 -36714.7 449095 -0.0817526 -32726.5 182.407 -21.8643 -84452.1 1.52624e+06 -0.0553335 0 0 0 -1 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan 1zzn_crystalstr_renum.pdb 58.266 0 -85.863 -65.022 -65.376 -280.714 -52.962 -792.917 217.358 61.824 -110.995 -1144.09 0 0 30.575 0 nan 26.0457 3.98531 -1 nan 0 -1475.5 -2.011 0 5.701 25.135 -1342.34 41.789 -642.024 11.416 -341.397 83.719 -29.914 695.074 19.352 -28.1007 3314 -0.00847939 24.5979 6.66684 -7.90459 -19311.4 205187 -0.094116 -17785 94.3432 -16.1786 -43028.6 468162 -0.0919096 -38597.3 182.237 -24.3163 -94975.1 1.57833e+06 -0.0601744 0 0 0 -1 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan 1zzn-on-1y0q_ModeRNA.pdb 125.054 0 -66.198 -55.954 -59.316 -192.569 -51.784 -625.984 262.445 632.178 -125.728 -253.475 0 0 29.434 0 0 -444.92 15.414 -87.819 166.97 -627.304 -122.06 -56.486 -95.613 -53.224 -299.921 nan -444.92 nan 3.07103 41047.3 22277.5 20284.8 12.3297 0 0 0.00265083 0 83621.9 3.78032e-09 83621.9 nan 0 -844.124 -1.99 0 7.65 29.734 -623.133 56.586 -518.743 15.024 -338.005 99.757 -95.224 492.854 31.367 21.4962 3280 0.00655372 57.2332 7.75972 -4.60545 -15610.7 204303 -0.0764096 -14493.5 101.499 -11.0073 -34992.5 465023 -0.075249 -31551.7 186.335 -18.4657 -68044.8 1.56905e+06 -0.0433668 0 0 0 41047.3 22277.5 20284.8 12.3297 0 0 -0.00169079 0 83621.9 3.78032e-09 83621.9 [5 rows x 94 columns] deeplearning prediction progress: [ (failed) H2O session _sid_9279 closed.