mqaprna.py ver: 89de82d-dirty start 2022-07-27 14:37:02 -------------------------- ---------------------------------------------------- Seq ss fn /home/mqapRNA/mqapRNAweb/media/jobs/e32fb463-3955-4113-b036-c223e9433c7f/ss.txt Output csv /home/mqapRNA/mqapRNAweb/media/jobs/e32fb463-3955-4113-b036-c223e9433c7f/e32fb46_raw.csv Input files #1 ['input/ms_0.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,RNA3DCNN,Dfire rmsd biopython_all Native pdb off RASP all -------------------------- ---------------------------------------------------- AnalyzeGeometry on SSAgreement on pdb_id >seq ref_seq GCUAGCAGGUCAGUGUGAACGCAAGCGAGAGCGCUGCCCUGCUAGCAAAAGCUAGCAGGGCAGCGCUCUCGCAAGCGUAUCACUACACCUGCUAGCAAAAGCUAGCAGGUGUAGUGAUACGCAAGCGAUGAACGUAGGGUGCUAGCAAAAGCUAGCACCCUACGUUCAUCGCAAGCGUUCACACUGACCUGCUAGCAAAA ref_ss ((((((((((((((((((((((..((((((((((((((((((((((....))))))))))))))))))))))..((((((((((((((((((((((....))))))))))))))))))))))..((((((((((((((((((((((....))))))))))))))))))))))..)))))))))))))))))))))).... to ignore 0 [] files to analyze: 1 ['input/ms_0.pdb'] -------------------------------------------------------------------------------- in: /home/mqapRNA/mqapRNAweb/media/jobs/e32fb463-3955-4113-b036-c223e9433c7f/e32fb46_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/tmp3ygOTV JVM stdout: /tmp/tmp3ygOTV/h2o_unknownUser_started_from_python.out JVM stderr: /tmp/tmp3ygOTV/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 (5 years, 3 months and 7 days)! Please download and install the latest version from http://h2o.ai/download/ -------------------------- ---------------------------------- H2O cluster uptime: 02 secs H2O cluster version: 3.10.4.5 H2O cluster version age: 5 years, 3 months and 7 days !!! H2O cluster name: H2O_from_python_unknownUser_wwr5fk H2O cluster total nodes: 1 H2O cluster free memory: 1.734 Gb H2O cluster total cores: 4 H2O cluster allowed cores: 4 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 rna3dcnn dfire ---- ------------- ------------------ --------------------- ----------------------------- --------------------------- ------------------------ ---------------------- --------------------- --------------------- --------------- ------------------------- -------------------- ------------------------- ------------------------- -------------- ---------------------------- -------------- --------------------- ------------------ ----------------------- ---------------------- ----------------------- ---------------------- ---------------------- ------------------------ ------------------------ ----------------------- ----------------------- --------------------- ------------ -------- ------------ ------------- 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----------------- ---------------- ----------------- ---------------------- ------------------------ ---------------- --------------------- ----------------- ---------------------- --------------------- ---------------------- ------------------------ ---------- ------- [0 rows x 96 columns] deeplearning prediction progress: [#######################################] 100% deeplearning prediction progress: [#######################################] 100% mqapRNA --------- [0 rows x 1 column] fn ---- [0 rows x 1 column] Exporting to /home/mqapRNA/mqapRNAweb/media/jobs/e32fb463-3955-4113-b036-c223e9433c7f/e32fb46_raw_mqapRNA.csv Export File progress: [###################################################] 100% Empty DataFrame Columns: [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, rna3dcnn, dfire, mqapRNA] Index: [] [0 rows x 96 columns] Empty DataFrame Columns: [mqapRNA] Index: [] saved /home/mqapRNA/mqapRNAweb/media/jobs/e32fb463-3955-4113-b036-c223e9433c7f/e32fb46_mqapRNA.csv H2O session _sid_9001 closed.