mqaprna.py ver: 5ab0ce1-dirty start 2017-07-05 14:49:06 -------------------------- ---------------------------------------------------- Seq ss fn /home/mqapRNA/mqapRNAweb/media/jobs/1303254f-e6d0-4bed-af2e-8feffa8d26e0/ss.txt Output csv /home/mqapRNA/mqapRNAweb/media/jobs/1303254f-e6d0-4bed-af2e-8feffa8d26e0/1303254_raw.csv Input files #1 ['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: 1 ['input/17_Major_6_rpr.pdb'] -------------------------------------------------------------------------------- [--------------------------------------------------------------------------------] 1 100.0 % 1 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', '-270.937', '-0.314', '0.0', '2.259', '7.688', '-234.037', '11.288', '-142.794', '3.993', '-88.851', '15.707', '-2.791', '127.027', '29.89'], 'RNAscore': 24.4173, 'RASP': ['2.993', '757', '0.00395376', '4.9618', '3.24122', '-0.607427', '-2982.08', '44679', '-0.0667446', '-2938.51', '38.7128', '-1.12537', '-6128.49', '104153', '-0.0588412', '-6089.31', '75.8194', '-0.51669', '-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/1303254f-e6d0-4bed-af2e-8feffa8d26e0/ss.txt -m 6 -f -o /home/mqapRNA/mqapRNAweb/media/jobs/1303254f-e6d0-4bed-af2e-8feffa8d26e0/1303254_raw.csv input/17_Major_6_rpr.pdb Execution time: 0:03:48.353 process: 6 start: 14:49:06 end: 14:52:55 Output: /home/mqapRNA/mqapRNAweb/media/jobs/1303254f-e6d0-4bed-af2e-8feffa8d26e0/1303254_raw.csv logging: /home/mqapRNA/mqapRNAweb/media/jobs/1303254f-e6d0-4bed-af2e-8feffa8d26e0/1303254_raw.log logging wrappers /home/mqapRNA/mqaprna_env/log/ in: /home/mqapRNA/mqapRNAweb/media/jobs/1303254f-e6d0-4bed-af2e-8feffa8d26e0/1303254_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 7 hours 25 mins H2O cluster version: 3.10.4.5 H2O cluster version age: 2 months and 16 days H2O cluster name: magnus H2O cluster total nodes: 1 H2O cluster free memory: 1.440 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 --------- 3.44925 [1 row x 1 column] fn ------------------ 17_Major_6_rpr.pdb [1 row x 1 column] Exporting to /home/mqapRNA/mqapRNAweb/media/jobs/1303254f-e6d0-4bed-af2e-8feffa8d26e0/1303254_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 farna_rna_backbone_backbone farna_rna_base_stack_axis \ fn 17_Major_6_rpr.pdb -21.407 -6.439 farna_rna_base_stagger farna_rna_base_stack \ fn 17_Major_6_rpr.pdb -59.165 -6.805 farna_rna_base_pair farna_rna_repulsive farna_rna_vdw \ fn 17_Major_6_rpr.pdb -167.109 53.658 13.997 ... rnakb_proper_dih_all rnakb_improper_dih_all \ fn ... 17_Major_6_rpr.pdb ... 6094.87 16.3691 rnakb_lj14_all rnakb_coulomb14_all rnakb_lj_sr_all \ fn 17_Major_6_rpr.pdb 0 0 -0.000491 rnakb_coulomb_sr_all rnakb_potential_all \ fn 17_Major_6_rpr.pdb 0 16002.5 rnakb_kinetic_en_all rnakb_total_energy_all mqapRNA fn 17_Major_6_rpr.pdb 9.692650e-10 16002.5 3.449247 [1 rows x 94 columns] mqapRNA fn 17_Major_6_rpr.pdb 3.449247 saved /home/mqapRNA/mqapRNAweb/media/jobs/1303254f-e6d0-4bed-af2e-8feffa8d26e0/1303254_mqapRNA.csv ploting H2O session _sid_9ac8 closed.