mqaprna.py ver: 48b2d0c-dirty start 2017-07-14 14:29:09 -------------------------- ---------------------------------------------------- Seq ss fn /home/mqapRNA/mqapRNAweb/media/jobs/9cf0fa05-9f98-4675-b8ba-3219dca4ab03/ss.txt Output csv /home/mqapRNA/mqapRNAweb/media/jobs/9cf0fa05-9f98-4675-b8ba-3219dca4ab03/9cf0fa0_raw.csv Input files #5 ['input/17_Bujnicki_7_rpr.pdb', 'input/17_Das_1_rpr.pdb', 'input/17_Das_4_rpr.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 CGUGGUUAGGGCCACGUUAAAUAGUUGCUUAAGCCCUAAGCGUUGAUAAAUAUCAGGUGCAA ref_ss ((((.[[[[[[.))))........((((.....]]]]]]...(((((....)))))..)))) to ignore 0 [] files to analyze: 5 ['input/17_Bujnicki_7_rpr.pdb', 'input/17_Das_1_rpr.pdb', 'input/17_Das_4_rpr.pdb', 'input/17_Dohkolyan_1_rpr.pdb', 'input/17_Major_6_rpr.pdb'] -------------------------------------------------------------------------------- [---------------- ] 1 20.0 % 5 10 True 17_Das_4_rpr.pdb {'AnalyzeGeometry': 22.5806, 'eSCORE': 1.43315, 'FARNA': ['-26.525', '-1.027', '-17.909', '-108.973', '-14.302', '-221.889', '13.636', '0.96', '-11.373', '-368.764', '0.0', '0.0', '18.638', '0.0'], 'ClashScore': 15.577889, 'length': 62, 'SimRNA_0': ['0', '-547.921961', '-298.538', '-84.436', '-1.117', '-248.266965', '-44.125', '-40.615', '-28.469', '-29.506', '-105.552', '', '-547.921961'], 'FARNA_hires': ['0.0', '-356.837', '-0.153', '0.0', '1.461', '4.543', '-314.55', '8.672', '-148.481', '2.224', '-90.612', '16.314', '-9.024', '168.925', '3.841'], 'RNAscore': 16.5026, 'RASP': ['-0.6548', '636', '-0.00102956', '5.20318', '2.53828', '-2.30785', '-5511.89', '39337', '-0.14012', '-5293.55', '41.0074', '-5.32442', '-12670.2', '89379', '-0.141758', '-11933.4', '77.2849', '-9.53417', '-29371.8', '309432', '-0.0949216', '0', '0', '0'], 'RNAkb': ['5.98349e+03', '2.50340e+03', '5.66775e+03', '6.23377e-01', '0.00000e+00', '0.00000e+00', '-2.05920e-03', '0.00000e+00', '1.41553e+04', '9.50833e-10', '1.41553e+04'], 'RNAkb_all': ['5.98349e+03', '2.50340e+03', '5.66775e+03', '6.23377e-01', '0.00000e+00', '0.00000e+00', '-7.84210e-04', '0.00000e+00', '1.41553e+04', '9.50833e-10', '1.41553e+04'], 'SSAgreement': '0.975'} [-------------------------------- ] 2 40.0 % 5 10 True 17_Das_1_rpr.pdb {'AnalyzeGeometry': 17.7419, 'eSCORE': 1.43655, 'FARNA': ['-25.941', '-0.781', '-20.339', '-102.772', '-15.772', '-210.313', '10.926', '0.849', '-13.508', '-357.486', '0.0', '0.0', '20.165', '0.0'], 'ClashScore': 8.542714, 'length': 62, 'SimRNA_0': ['0', '-577.595885', '-304.467', '-96.772', '-0.145', '-272.983295', '-49.021', '-47.144', '-32.107', '-35.486', '-109.226', '', '-577.595885'], 'FARNA_hires': ['0.0', '-359.206', '0.0', '0.0', '1.471', '5.196', '-305.984', '7.254', '-156.252', '2.305', '-87.686', '12.931', '-4.166', '162.618', '3.105'], 'RNAscore': 16.1099, 'RASP': ['-3.1964', '583', '-0.00548268', '4.67952', '2.82315', '-2.78976', '-5591.36', '36005', '-0.155294', '-5300.96', '37.4664', '-7.75098', '-12988.6', '81838', '-0.158711', '-12091.9', '75.2502', '-11.9162', '-30282.5', '283765', '-0.106717', '0', '0', '0'], 'RNAkb': ['5.96636e+03', '2.50310e+03', '5.72950e+03', '6.46352e-01', '0.00000e+00', '0.00000e+00', '-1.54358e-03', '0.00000e+00', '1.41996e+04', '9.48439e-10', '1.41996e+04'], 'RNAkb_all': ['5.96636e+03', '2.50310e+03', '5.72950e+03', '6.46352e-01', '0.00000e+00', '0.00000e+00', '-7.57241e-04', '0.00000e+00', '1.41996e+04', '9.48439e-10', '1.41996e+04'], 'SSAgreement': '0.975'} [------------------------------------------------ ] 3 60.0 % 5 10 True 17_Bujnicki_7_rpr.pdb {'AnalyzeGeometry': 11.2903, 'eSCORE': 1.40036, 'FARNA': ['-26.41', '-5.748', '-18.393', '-104.358', '-14.32', '-215.78', '7.509', '6.818', '-7.173', '-359.656', '0.0', '0.0', '18.198', '0.0'], 'ClashScore': 1.507538, 'length': 62, 'SimRNA_0': ['0', '-536.728354', '-283.215', '-80.145', '-0.846', '-252.667248', '-37.963', '-47.092', '-36.305', '-27.303', '-104.003', '', '-536.728354'], 'FARNA_hires': ['0.0', '-296.586', '-1.87', '0.0', '1.195', '7.668', '-272.229', '7.609', '-140.549', '2.357', '-78.84', '10.195', '-6.769', '171.206', '3.44'], 'RNAscore': 17.3346, 'RASP': ['-1.5117', '640', '-0.00236203', '6.30497', '3.66108', '-2.13507', '-5280.66', '38946', '-0.135589', '-4997.86', '37.9906', '-7.44401', '-11803.8', '88867', '-0.132825', '-10950', '75.1242', '-11.3651', '-26922.2', '300533', '-0.0895815', '0', '0', '0'], 'RNAkb': ['6.63748e+03', '4.08482e+03', '5.46709e+03', '1.25895e+00', '0.00000e+00', '0.00000e+00', '-1.04038e-03', '0.00000e+00', '1.61906e+04', '9.94050e-10', '1.61906e+04'], 'RNAkb_all': ['6.63748e+03', '4.08482e+03', '5.46709e+03', '1.25895e+00', '0.00000e+00', '0.00000e+00', '-7.12617e-04', '0.00000e+00', '1.61906e+04', '9.94050e-10', '1.61906e+04'], 'SSAgreement': '0.975'} [---------------------------------------------------------------- ] 4 80.0 % 5 10 True 17_Dohkolyan_1_rpr.pdb {'AnalyzeGeometry': 30.6452, 'eSCORE': 0.86939, 'FARNA': ['-15.723', '-5.488', '-5.096', '-53.816', '-5.149', '-185.122', '13.116', '13.214', '-15.346', '-237.606', '0.0', '0.0', '21.803', '0.0'], 'ClashScore': 23.61809, 'length': 62, 'SimRNA_0': ['0', '-411.437674', '-155.543', '-60.544', '4.715', '-260.609821', '-48.614', '-52.227', '-39.264', '-30.590', '-89.914', '', '-411.437674'], 'FARNA_hires': ['0.0', '-234.484', '-1.808', '0.0', '1.534', '15.377', '-217.655', '9.049', '-137.537', '1.368', '-85.604', '10.77', '-17.58', '178.407', '9.196'], 'RNAscore': 18.8536, 'RASP': ['5.606', '636', '0.00881447', '5.93976', '2.45041', '-0.136206', '-5369.01', '37749', '-0.142229', '-5230.13', '32.4445', '-4.28042', '-12368.4', '88312', '-0.140053', '-11991.7', '70.37', '-5.35186', '-24195.1', '310238', '-0.0779888', '0', '0', '0'], 'RNAkb': ['6.51020e+03', '4.31257e+03', '7.69595e+03', '2.52520e+02', '0.00000e+00', '0.00000e+00', '-1.65685e-03', '0.00000e+00', '1.87712e+04', '1.01573e-09', '1.87712e+04'], 'RNAkb_all': ['6.51020e+03', '4.31257e+03', '7.69595e+03', '2.52520e+02', '0.00000e+00', '0.00000e+00', '-5.62285e-04', '0.00000e+00', '1.87712e+04', '1.01573e-09', '1.87712e+04'], 'SSAgreement': '0.533'} [--------------------------------------------------------------------------------] 5 100.0 % 5 10 True 17_Major_6_rpr.pdb {'AnalyzeGeometry': 51.6129, 'eSCORE': 0.58693, 'FARNA': ['-12.245', '-21.407', '-6.439', '-59.165', '-6.805', '-167.109', '53.658', '13.997', '-24.34', '-212.943', '0.0', '0.0', '16.912', '0.0'], 'ClashScore': 3.015075, 'length': 62, 'SimRNA_0': ['0', '-213.643135', '-82.771', '-17.374', '0.912', '-131.784132', '-36.482', '-36.334', '-28.376', '4.459', '-35.051', '', '-213.643135'], 'FARNA_hires': ['0.0', '-270.911', '-0.315', '0.0', '2.259', '7.679', '-233.986', '11.287', '-142.774', '3.988', '-88.829', '15.689', '-2.789', '126.992', '29.886'], 'RNAscore': 24.4173, 'RASP': ['2.993', '757', '0.00395376', '7.19458', '3.58168', '-1.17307', '-2982.08', '44679', '-0.0667446', '-2936.81', '39.3651', '-1.14988', '-6128.49', '104153', '-0.0588412', '-6097.45', '74.3024', '-0.417653', '-9883.01', '353719', '-0.0279403', '0', '0', '0'], 'RNAkb': ['6.10016e+03', '3.79112e+03', '6.09487e+03', '1.63691e+01', '0.00000e+00', '0.00000e+00', '1.60955e-03', '0.00000e+00', '1.60025e+04', '9.69265e-10', '1.60025e+04'], 'RNAkb_all': ['6.10016e+03', '3.79112e+03', '6.09487e+03', '1.63691e+01', '0.00000e+00', '0.00000e+00', '-4.90915e-04', '0.00000e+00', '1.60025e+04', '9.69265e-10', '1.60025e+04'], 'SSAgreement': '0.509'} Cmd: mqaprna.py -s /home/mqapRNA/mqapRNAweb/media/jobs/9cf0fa05-9f98-4675-b8ba-3219dca4ab03/ss.txt -m 6 -f -o /home/mqapRNA/mqapRNAweb/media/jobs/9cf0fa05-9f98-4675-b8ba-3219dca4ab03/9cf0fa0_raw.csv input/17_Bujnicki_7_rpr.pdb input/17_Das_1_rpr.pdb input/17_Das_4_rpr.pdb input/17_Dohkolyan_1_rpr.pdb input/17_Major_6_rpr.pdb Execution time: 0:03:52.983 process: 6 start: 14:29:09 end: 14:33:02 Output: /home/mqapRNA/mqapRNAweb/media/jobs/9cf0fa05-9f98-4675-b8ba-3219dca4ab03/9cf0fa0_raw.csv logging: /home/mqapRNA/mqapRNAweb/media/jobs/9cf0fa05-9f98-4675-b8ba-3219dca4ab03/9cf0fa0_raw.log logging wrappers /home/mqapRNA/mqaprna_env/log/ in: /home/mqapRNA/mqapRNAweb/media/jobs/9cf0fa05-9f98-4675-b8ba-3219dca4ab03/9cf0fa0_raw.csv model_key: grid-8a6dfea4-1f6e-4354-9396-f727a5bd937a_model_14 Checking whether there is an H2O instance running at http://localhost:54321..... not found. Attempting to start a local H2O server... Java Version: java version "1.8.0_131"; Java(TM) SE Runtime Environment (build 1.8.0_131-b11); Java HotSpot(TM) 64-Bit Server VM (build 25.131-b11, mixed mode) Starting server from /usr/local/lib/python2.7/dist-packages/h2o/backend/bin/h2o.jar Ice root: /tmp/tmpvpEYP3 JVM stdout: /tmp/tmpvpEYP3/h2o_unknownUser_started_from_python.out JVM stderr: /tmp/tmpvpEYP3/h2o_unknownUser_started_from_python.err Server is running at http://127.0.0.1:54321 Connecting to H2O server at http://127.0.0.1:54321... successful. -------------------------- ---------------------------------- H2O cluster uptime: 04 secs H2O cluster version: 3.10.4.5 H2O cluster version age: 2 months and 24 days H2O cluster name: H2O_from_python_unknownUser_h9f7fu H2O cluster total nodes: 1 H2O cluster free memory: 1.742 Gb H2O cluster total cores: 8 H2O cluster allowed cores: 8 H2O cluster status: accepting new members, healthy H2O connection url: http://127.0.0.1:54321 H2O connection proxy: H2O internal security: False Python version: 2.7.6 final -------------------------- ---------------------------------- Parse progress: [#########################################################] 100% deeplearning prediction progress: [#######################################] 100% deeplearning prediction progress: [#######################################] 100% mqapRNA --------- 1.53956 1.2689 1.51471 3.77803 3.52932 [5 rows x 1 column] fn ---------------------- 17_Das_4_rpr.pdb 17_Das_1_rpr.pdb 17_Bujnicki_7_rpr.pdb 17_Dohkolyan_1_rpr.pdb 17_Major_6_rpr.pdb [5 rows x 1 column] Exporting to /home/mqapRNA/mqapRNAweb/media/jobs/9cf0fa05-9f98-4675-b8ba-3219dca4ab03/9cf0fa0_raw_mqapRNA.csv Export File progress: [###################################################] 100% clash_score analyze_geometry farna_rna_base_axis \ fn 17_Das_1_rpr.pdb 8.542714 17.7419 -25.941 17_Bujnicki_7_rpr.pdb 1.507538 11.2903 -26.410 17_Das_4_rpr.pdb 15.577889 22.5806 -26.525 17_Major_6_rpr.pdb 3.015075 51.6129 -12.245 17_Dohkolyan_1_rpr.pdb 23.618090 30.6452 -15.723 farna_rna_backbone_backbone \ fn 17_Das_1_rpr.pdb -0.781 17_Bujnicki_7_rpr.pdb -5.748 17_Das_4_rpr.pdb -1.027 17_Major_6_rpr.pdb -21.407 17_Dohkolyan_1_rpr.pdb -5.488 farna_rna_base_stack_axis farna_rna_base_stagger \ fn 17_Das_1_rpr.pdb -20.339 -102.772 17_Bujnicki_7_rpr.pdb -18.393 -104.358 17_Das_4_rpr.pdb -17.909 -108.973 17_Major_6_rpr.pdb -6.439 -59.165 17_Dohkolyan_1_rpr.pdb -5.096 -53.816 farna_rna_base_stack farna_rna_base_pair \ fn 17_Das_1_rpr.pdb -15.772 -210.313 17_Bujnicki_7_rpr.pdb -14.320 -215.780 17_Das_4_rpr.pdb -14.302 -221.889 17_Major_6_rpr.pdb -6.805 -167.109 17_Dohkolyan_1_rpr.pdb -5.149 -185.122 farna_rna_repulsive farna_rna_vdw ... \ fn ... 17_Das_1_rpr.pdb 10.926 0.849 ... 17_Bujnicki_7_rpr.pdb 7.509 6.818 ... 17_Das_4_rpr.pdb 13.636 0.960 ... 17_Major_6_rpr.pdb 53.658 13.997 ... 17_Dohkolyan_1_rpr.pdb 13.116 13.214 ... rnakb_proper_dih_all rnakb_improper_dih_all \ fn 17_Das_1_rpr.pdb 5729.50 0.646352 17_Bujnicki_7_rpr.pdb 5467.09 1.258950 17_Das_4_rpr.pdb 5667.75 0.623377 17_Major_6_rpr.pdb 6094.87 16.369100 17_Dohkolyan_1_rpr.pdb 7695.95 252.520000 rnakb_lj14_all rnakb_coulomb14_all rnakb_lj_sr_all \ fn 17_Das_1_rpr.pdb 0 0 -0.000757 17_Bujnicki_7_rpr.pdb 0 0 -0.000713 17_Das_4_rpr.pdb 0 0 -0.000784 17_Major_6_rpr.pdb 0 0 -0.000491 17_Dohkolyan_1_rpr.pdb 0 0 -0.000562 rnakb_coulomb_sr_all rnakb_potential_all \ fn 17_Das_1_rpr.pdb 0 14199.6 17_Bujnicki_7_rpr.pdb 0 16190.6 17_Das_4_rpr.pdb 0 14155.3 17_Major_6_rpr.pdb 0 16002.5 17_Dohkolyan_1_rpr.pdb 0 18771.2 rnakb_kinetic_en_all rnakb_total_energy_all mqapRNA fn 17_Das_1_rpr.pdb 9.484390e-10 14199.6 1.268902 17_Bujnicki_7_rpr.pdb 9.940500e-10 16190.6 1.514708 17_Das_4_rpr.pdb 9.508330e-10 14155.3 1.539558 17_Major_6_rpr.pdb 9.692650e-10 16002.5 3.529324 17_Dohkolyan_1_rpr.pdb 1.015730e-09 18771.2 3.778034 [5 rows x 94 columns] mqapRNA fn 17_Das_1_rpr.pdb 1.268902 17_Bujnicki_7_rpr.pdb 1.514708 17_Das_4_rpr.pdb 1.539558 17_Major_6_rpr.pdb 3.529324 17_Dohkolyan_1_rpr.pdb 3.778034 saved /home/mqapRNA/mqapRNAweb/media/jobs/9cf0fa05-9f98-4675-b8ba-3219dca4ab03/9cf0fa0_mqapRNA.csv H2O session _sid_915e closed. ploting