mqaprna.py ver: 8fc5197-dirty start 2017-07-05 07:53:02 -------------------------- ---------------------------------------------------- Seq ss fn /home/mqapRNA/mqapRNAweb/media/jobs/22114a5a-7eec-406f-999b-08d3680b1e71/ss.txt Output csv /home/mqapRNA/mqapRNAweb/media/jobs/22114a5a-7eec-406f-999b-08d3680b1e71/22114a5_raw.csv Input files #2 ['input/17_Dohkolyan_1_rpr.pdb', 'input/17_Major_6_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 ref_ss ..((.(((((((....................))))))).))(((((....)))))...... to ignore 0 [] files to analyze: 2 ['input/17_Dohkolyan_1_rpr.pdb', 'input/17_Major_6_rpr.pdb'] -------------------------------------------------------------------------------- [---------------------------------------- ] 1 50.0 % 2 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': 0, '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', '6.08361', '3.21102', '-0.14874', '-5369.01', '37749', '-0.142229', '-5231.24', '35.3359', '-3.89884', '-12368.4', '88312', '-0.140053', '-11981.5', '69.8589', '-5.53785', '-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': '0.345'} [--------------------------------------------------------------------------------] 2 100.0 % 2 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': 0, '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', '-272.798', '-0.373', '0.0', '2.493', '7.926', '-231.603', '12.324', '-144.355', '4.121', '-91.993', '15.009', '-3.029', '126.077', '30.605'], 'RNAscore': 24.4173, 'RASP': ['2.993', '757', '0.00395376', '6.28052', '3.45778', '-0.950758', '-2982.08', '44679', '-0.0667446', '-2934.79', '35.0895', '-1.34755', '-6128.49', '104153', '-0.0588412', '-6089.33', '74.8365', '-0.523276', '-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': '0.371'} Cmd: mqaprna.py -s /home/mqapRNA/mqapRNAweb/media/jobs/22114a5a-7eec-406f-999b-08d3680b1e71/ss.txt -m 6 -f -o /home/mqapRNA/mqapRNAweb/media/jobs/22114a5a-7eec-406f-999b-08d3680b1e71/22114a5_raw.csv input/17_Dohkolyan_1_rpr.pdb input/17_Major_6_rpr.pdb Execution time: 0:05:19.692 process: 6 start: 07:53:02 end: 07:58:22 Output: /home/mqapRNA/mqapRNAweb/media/jobs/22114a5a-7eec-406f-999b-08d3680b1e71/22114a5_raw.csv logging: /home/mqapRNA/mqapRNAweb/media/jobs/22114a5a-7eec-406f-999b-08d3680b1e71/22114a5_raw.log logging wrappers /home/mqapRNA/mqaprna_env/log/ in: /home/mqapRNA/mqapRNAweb/media/jobs/22114a5a-7eec-406f-999b-08d3680b1e71/22114a5_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. -------------------------- ----------------------- H2O cluster uptime: 14 days 0 hours 31 mins H2O cluster version: 3.10.4.5 H2O cluster version age: 2 months and 15 days H2O cluster name: magnus H2O cluster total nodes: 1 H2O cluster free memory: 1.407 Gb 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% deeplearning prediction progress: [#######################################] 100% deeplearning prediction progress: [#######################################] 100% mqapRNA --------- 3.75644 3.51229 [2 rows x 1 column] fn ---------------------- 17_Dohkolyan_1_rpr.pdb 17_Major_6_rpr.pdb [2 rows x 1 column] Exporting to /home/mqapRNA/mqapRNAweb/media/jobs/22114a5a-7eec-406f-999b-08d3680b1e71/22114a5_raw_mqapRNA.csv Export File progress: [###################################################] 100% clash_score analyze_geometry farna_rna_base_axis \ fn 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_Major_6_rpr.pdb -21.407 17_Dohkolyan_1_rpr.pdb -5.488 farna_rna_base_stack_axis farna_rna_base_stagger \ fn 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_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_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_Major_6_rpr.pdb 6094.87 16.3691 17_Dohkolyan_1_rpr.pdb 7695.95 252.5200 rnakb_lj14_all rnakb_coulomb14_all rnakb_lj_sr_all \ fn 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_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_Major_6_rpr.pdb 9.692650e-10 16002.5 3.512289 17_Dohkolyan_1_rpr.pdb 1.015730e-09 18771.2 3.756441 [2 rows x 94 columns] mqapRNA fn 17_Major_6_rpr.pdb 3.512289 17_Dohkolyan_1_rpr.pdb 3.756441 saved /home/mqapRNA/mqapRNAweb/media/jobs/22114a5a-7eec-406f-999b-08d3680b1e71/22114a5_mqapRNA.csv ploting H2O session _sid_9926 closed.