mqaprna.py ver: f69479e-dirty start 2018-06-30 20:15:16 -------------------------- ---------------------------------------------------- Seq ss fn /home/mqapRNA/mqapRNAweb/media/jobs/142ba8b8-c9fd-4e60-b8eb-e62e76a51d4f/ss.txt Output csv /home/mqapRNA/mqapRNAweb/media/jobs/142ba8b8-c9fd-4e60-b8eb-e62e76a51d4f/142ba8b_raw.csv Input files #1 ['input/18S_C.parvum.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 AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACUUUUAUACGGUUAAACUGCGAAUGGCUCAUUAUAACAGUUAUAGUUUACUUGAUAAUCUUUACUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCGAAAAAACUCGACUUUAUGGAAGGGUUGUAUUUAUUAGAUAAAGAACCAAUAUAAUUGGUGACUCAUAAUAACUUUACGGAUCACAUUAAAUGUGACAUAUCAUUCAAGUUUCUGACCUAUCAGCUUUAGACGGUAGGGUAUUGGCCUACCGUGGCAAUGACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGACUUUUUGGUUUUGUAAUUGGAAUGAGUUAAGUAUAAACCCCUUUACAAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGUUAAUAAUUUAUAUAAAAUAUUUUGAUGAAUAUUUAUAUAAUAUUAACAUAAUUCAUAUUACUAUAUAUUUUAGUAUAUGAAAUUUUACUUUGAGAAAAUUAGAGUGCUUAAAGCAGGCAUAUGCCUUGAAUACUCCAGCAUGGAAUAAUAUUAAAGAUUUUUAUCUUUCUUAUUGGUUCUAAGAUAAGAAUAAUGAUUAAUAGGGACAGUUGGGGGCAUUUGUAUUUAACAGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACAAACUAAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCAACUAGAGAUUGGAGGUUGUUCCUUACUCCUUCAGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACCAGGUCCAGACAUAGGAAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUAGACAUAAGAAAUAUUAUAUUUUUUAUCUGUCUUCUUAGAGGGACUUUGUAUGUUUAAUACAGGGAAGUUUUAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCGCGCGCGCUACACUGAUGCAUCCAUCAAGUAUAUAUUCCUGUUUCGAAGGAAAUGGGUAAUCUUUUGAAUAUGCAUCGUGAUGGGGAUAGAUCAUUGCAAUUAUUGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGCUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGAUCCGGUGAAUUAUUCGGACCAUACUUUGUAGCAAUACAUGUAAGGAAAGUUUCGUAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUC ref_ss ...(((((.......)))))........(.((((((.....(.....(((.(((.((((...((((((....)))))).................(((...................((((((.....(.......(((((....))))).....((((......((((.........(((((..((....))..)))))))))....))))......((((((...)))))).....................(((((.....))))).)......))))))......(((.......((..((((((((.......)))))))))).......)))...((((((((....))))...))))))).((.((((........)))).))............)))))))))).)....((((((...(((.......))).)))))))))))).).........((((((((.(((((...((((..........................))))....)))))((((((.......((((.....((....)).......))))))))))...(((((((((((((....((.........))..((((.((((((..(((((((...(((((((((.(((((....)))))))))))))).))))))).))))))..)))).....))))))))))))).......(((((((......(((.((((........((((((..(((((....(((((((......(((((..((((((....))))))..)))))(((((......))))).................)))))))...(((((..(((((((((.((((......)))).)).)))))))..)))))...((((....))))....)))))..((((...........))))....((((((....(...((((.........))))...).)))))).......)))))).........(.(((((............)))))))))).))).......)))))))....)))))))).(((......((((....))))....)))........(((((.(((((((..((.((((((...((.((((((.........(((.....)))........(((((.(....(((((((((.(..((............))..))))...))))))...((.((((..((((((((....(((((((((((.(..........).)))))))))))..............(((.((((..(((((.((((((((...))))))))...)))))..)))).))).((((((((.....))))))))..............))).)))...).))))))).....).))))))))))).))......(((.(((((((.....(((.....(((((((((((....)))))))).))))))......))))))))))...(....((((((..........))))))....).....))))))....((((((((.(....)))))))))......))...)))))))))).))....(..((...(((((.....(((((((((..(((..((.(..(...((......((((....)))).....))...)..).))..)))..)))))))))....)))))....))...)....((((((((((....))))))))))........ to ignore 0 [] files to analyze: 1 ['input/18S_C.parvum.pdb'] -------------------------------------------------------------------------------- [--------------------------------------------------------------------------------] 1 100.0 % 1 10 True 18S_C.parvum.pdb {'AnalyzeGeometry': 2.6482, 'eSCORE': 24.56015, 'FARNA': ['-472.999', '-488.784', '-388.626', '-1587.311', '-316.77', '-4903.785', '1681.635', '1402.23', '-1000.511', '-6005.568', '0.0', '0.0', '69.354', '0.0'], 'ClashScore': 18.554635, 'length': 1749, 'SimRNA_0': ['0', '-9424.355575', '-3943.310', '-1707.644', '111.768', '-5592.813419', '-1149.349', '-516.894', '-935.201', '-592.232', '-2399.137', '', '-9424.355575'], 'FARNA_hires': 'error', 'RNAscore': nan, 'RASP': 'error', 'RNAkb': 255, 'RNAkb_all': 'error', 'SSAgreement': 'error'} Cmd: mqaprna.py -s /home/mqapRNA/mqapRNAweb/media/jobs/142ba8b8-c9fd-4e60-b8eb-e62e76a51d4f/ss.txt -m 6 -f -o /home/mqapRNA/mqapRNAweb/media/jobs/142ba8b8-c9fd-4e60-b8eb-e62e76a51d4f/142ba8b_raw.csv input/18S_C.parvum.pdb Execution time: 1:13:58.315 process: 6 start: 20:15:16 end: 21:29:14 Output: /home/mqapRNA/mqapRNAweb/media/jobs/142ba8b8-c9fd-4e60-b8eb-e62e76a51d4f/142ba8b_raw.csv logging: /home/mqapRNA/mqapRNAweb/media/jobs/142ba8b8-c9fd-4e60-b8eb-e62e76a51d4f/142ba8b_raw.log logging wrappers /home/mqapRNA/mqaprna_env/log/ in: /home/mqapRNA/mqapRNAweb/media/jobs/142ba8b8-c9fd-4e60-b8eb-e62e76a51d4f/142ba8b_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/tmpQ6hURt JVM stdout: /tmp/tmpQ6hURt/h2o_unknownUser_started_from_python.out JVM stderr: /tmp/tmpQ6hURt/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. Warning: Your H2O cluster version is too old (1 year, 2 months and 11 days)! Please download and install the latest version from http://h2o.ai/download/ -------------------------- ---------------------------------- H2O cluster uptime: 03 secs H2O cluster version: 3.10.4.5 H2O cluster version age: 1 year, 2 months and 11 days !!! H2O cluster name: H2O_from_python_unknownUser_j2vqp0 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% 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 ---------------- ------------- ------------------ --------------------- ----------------------------- --------------------------- ------------------------ ---------------------- --------------------- --------------------- --------------- ------------------------- -------------------- ------------------------- ------------------------- -------------- ---------------------------- -------------- --------------------- ------------------ ----------------------- ---------------------- ----------------------- ---------------------- ---------------------- ------------------------ ------------------------ ----------------------- ----------------------- --------------------- ------------ -------- ------------ ------------- ------------------ -------------------- ------------ ----------------- ------------- ------------------ ----------------- ------------------ -------------------- ----------------- ---------------------------------- ------------------- ---------------------- ------------------------------- -------------------- ----------------------- ---------------- ------------------- -------------- ----------------------------- --------------- -------------- ---------------------- ---------------- ------------------- -------------------- --------------------- --------------------- --------------------- ------------------- ---------------- -------------------- --------------------- --------------------- --------------------- ------------------- ---------------- --------------------- ---------------------- ---------------------- ---------------------- -------------------- ----------------- --------------------- ---------------------- ---------------------- ---------------------- -------------------- ----------------- ---------------- ----------------- ---------------------- ------------------------ ---------------- --------------------- ----------------- ---------------------- --------------------- ---------------------- ------------------------ 18S_C.parvum.pdb 18.5546 2.6482 -472.999 -488.784 -388.626 -1587.31 -316.77 -4903.78 1681.63 1402.23 -1000.51 -6005.57 0 0 69.354 0 0 -9424.36 -3943.31 -1707.64 111.768 -5592.81 -1149.35 -516.894 -935.201 -592.232 -2399.14 nan -9424.36 nan 24.5602 255 error error error error 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 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 [1 row x 94 columns] deeplearning prediction progress: [ (failed) H2O session _sid_8e57 closed.