mqaprna.py ver: 52e618e-dirty start 2017-08-18 14:45:06 -------------------------- ---------------------------------------------------- Seq ss fn /home/mqapRNA/mqapRNAweb/media/jobs/9f6a45f7-1d0e-4b83-b8d5-2ed1b2d4f8ab/ss.txt Output csv /home/mqapRNA/mqapRNAweb/media/jobs/9f6a45f7-1d0e-4b83-b8d5-2ed1b2d4f8ab/9f6a45f_raw.csv Input files #5 ['input/UR1_1745_manA_cl1.pdb', 'input/UR1_1745_manA_cl2.pdb', 'input/UR1_1745_manA_cl3.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 GUUGGACGCAACAUGGGAGUGACUGAAUAAACUUACUGGCAACCGCUGGUUAAGGUGAUGAGACACAGGUGGUGCUGCUGCUCGCAAGGGUAGAACCGAUCAACCAAUCGGGUCUCAGGCAAUAACGUAUUUACUUACUGUAGUAAUGCCCGUUAUUUGUUGGUAUACAGGAAUCCAACCUCCCUCCU ref_ss ..............(((((...............((((((....))))))...(.(..((((((.............((((((....))))))..((((........))))))))))).)((((((....((((........)))).....)))))).(((((...........)))))))))).... to ignore 0 [] files to analyze: 5 ['input/UR1_1745_manA_cl1.pdb', 'input/UR1_1745_manA_cl2.pdb', 'input/UR1_1745_manA_cl3.pdb', 'input/UR1_1745_manA_cl4.pdb', 'input/UR1_1745_manA_cl5.pdb'] -------------------------------------------------------------------------------- [---------------- ] 1 20.0 % 5 10 True UR1_1745_manA_cl2.pdb {'AnalyzeGeometry': 27.1277, 'eSCORE': 3.77993, 'FARNA': ['-78.525', '-11.289', '-47.259', '-302.255', '-41.828', '-687.761', '168.306', '276.722', '-50.487', '-745.885', '0.0', '0.0', '28.493', '0.0'], 'ClashScore': 157.064586, 'length': 188, 'SimRNA_0': ['0', '-1370.529432', '-645.473', '-126.670', '-2.141', '-722.915631', '-60.122', '-158.208', '-100.544', '-73.259', '-330.783', '', '-1370.529432'], 'FARNA_hires': ['0.0', '-939.239', '-3.443', '0.0', '8.041', '30.94', '-832.635', '39.765', '-476.662', '10.099', '-271.142', '73.033', '-10.324', '464.285', '28.804'], 'RNAscore': 23.3323, 'RASP': ['13.49', '2561', '0.00526747', '28.4345', '5.85641', '-2.55182', '-14578.2', '159293', '-0.0915183', '-13693.9', '75.8109', '-11.6647', '-31190.7', '361346', '-0.0863182', '-29052.6', '143.896', '-14.8587', '-75219.5', '1192036', '-0.0631017', '0', '0', '0'], 'RNAkb': ['4.52241e+04', '3.54164e+04', '1.83745e+04', '6.65337e+01', '0.00000e+00', '0.00000e+00', '-1.51384e-03', '0.00000e+00', '9.90815e+04', '3.53693e-09', '9.90815e+04'], 'RNAkb_all': ['4.52241e+04', '3.54164e+04', '1.83745e+04', '6.65337e+01', '0.00000e+00', '0.00000e+00', '-1.70680e-03', '0.00000e+00', '9.90815e+04', '3.53693e-09', '9.90815e+04'], 'SSAgreement': '0.774'} [-------------------------------- ] 2 40.0 % 5 10 True UR1_1745_manA_cl5.pdb {'AnalyzeGeometry': 29.7872, 'eSCORE': 3.77645, 'FARNA': ['-80.239', '-20.253', '-47.277', '-296.488', '-40.082', '-690.285', '77.263', '180.275', '-51.52', '-936.302', '0.0', '0.0', '32.306', '0.0'], 'ClashScore': 123.692512, 'length': 188, 'SimRNA_0': ['0', '-1504.249488', '-726.942', '-197.622', '-5.801', '-771.506038', '-81.393', '-157.434', '-103.690', '-63.371', '-365.619', '', '-1504.249488'], 'FARNA_hires': ['0.0', '-893.527', '-4.98', '0.0', '6.845', '29.734', '-784.768', '41.427', '-481.89', '5.393', '-290.178', '88.826', '-25.708', '491.723', '30.049'], 'RNAscore': 23.5796, 'RASP': ['8.1346', '2269', '0.0035851', '20.6725', '5.73218', '-2.18728', '-14745.1', '140110', '-0.10524', '-14126.1', '65.531', '-9.44576', '-32994.6', '318740', '-0.103516', '-31238.4', '133.94', '-13.1117', '-75507.2', '1090452', '-0.0692439', '0', '0', '0'], 'RNAkb': ['5.73890e+04', '3.56759e+04', '1.85236e+04', '6.01855e+01', '0.00000e+00', '0.00000e+00', '-2.32803e-03', '0.00000e+00', '1.11649e+05', '3.85585e-09', '1.11649e+05'], 'RNAkb_all': ['5.73890e+04', '3.56759e+04', '1.85236e+04', '6.01855e+01', '0.00000e+00', '0.00000e+00', '-1.91369e-03', '0.00000e+00', '1.11649e+05', '3.85585e-09', '1.11649e+05'], 'SSAgreement': '0.705'} [------------------------------------------------ ] 3 60.0 % 5 10 True UR1_1745_manA_cl1.pdb {'AnalyzeGeometry': 35.6383, 'eSCORE': 3.70679, 'FARNA': ['-78.534', '-8.747', '-45.826', '-289.19', '-37.464', '-697.319', '150.141', '227.943', '-46.511', '-793.646', '0.0', '0.0', '31.861', '0.0'], 'ClashScore': 150.273677, 'length': 188, 'SimRNA_0': ['0', '-1470.298748', '-674.977', '-163.100', '2.597', '-797.918216', '-88.766', '-159.883', '-106.928', '-77.611', '-364.729', '', '-1470.298748'], 'FARNA_hires': ['0.0', '-892.915', '-4.996', '0.0', '6.259', '26.135', '-733.803', '38.425', '-475.599', '4.728', '-278.991', '76.503', '-34.732', '449.598', '33.557'], 'RNAscore': 23.4735, 'RASP': ['-0.0161', '2502', '-6.43485e-06', '20.8699', '6.64091', '-3.14505', '-14533.7', '155733', '-0.0933243', '-13803.5', '85.7511', '-8.51548', '-32027.3', '353793', '-0.0905255', '-30203.8', '142.856', '-12.7643', '-75412.3', '1197684', '-0.0629651', '0', '0', '0'], 'RNAkb': ['5.84026e+04', '3.31510e+04', '1.87026e+04', '6.08732e+01', '0.00000e+00', '0.00000e+00', '-1.70830e-03', '0.00000e+00', '1.10317e+05', '3.88071e-09', '1.10317e+05'], 'RNAkb_all': ['5.84026e+04', '3.31510e+04', '1.87026e+04', '6.08732e+01', '0.00000e+00', '0.00000e+00', '-1.99561e-03', '0.00000e+00', '1.10317e+05', '3.88071e-09', '1.10317e+05'], 'SSAgreement': '0.742'} [---------------------------------------------------------------- ] 4 80.0 % 5 10 True UR1_1745_manA_cl3.pdb {'AnalyzeGeometry': 27.1277, 'eSCORE': 3.65943, 'FARNA': ['-77.649', '-19.793', '-40.372', '-289.839', '-33.197', '-710.349', '129.972', '207.676', '-36.727', '-841.678', '0.0', '0.0', '28.6', '0.0'], 'ClashScore': 150.605407, 'length': 188, 'SimRNA_0': ['0', '-1483.945235', '-724.583', '-185.173', '-2.574', '-756.788136', '-80.836', '-161.095', '-83.720', '-63.899', '-367.238', '', '-1483.945235'], 'FARNA_hires': ['0.0', '-840.723', '-4.759', '0.0', '7.132', '28.738', '-682.09', '43.806', '-463.956', '3.759', '-290.466', '51.108', '-11.755', '446.142', '31.619'], 'RNAscore': 23.4328, 'RASP': ['-0.4082', '2502', '-0.000163149', '21.4822', '5.97659', '-3.66269', '-15070.2', '155779', '-0.0967409', '-13986.8', '68.9136', '-15.721', '-33276.1', '354973', '-0.0937427', '-30473.6', '140.502', '-19.9468', '-76881.3', '1196079', '-0.0642778', '0', '0', '0'], 'RNAkb': ['5.45778e+04', '3.77015e+04', '1.83409e+04', '7.80481e+01', '0.00000e+00', '0.00000e+00', '-1.58207e-03', '0.00000e+00', '1.10698e+05', '3.77342e-09', '1.10698e+05'], 'RNAkb_all': ['5.45778e+04', '3.77015e+04', '1.83409e+04', '7.80481e+01', '0.00000e+00', '0.00000e+00', '-1.83685e-03', '0.00000e+00', '1.10698e+05', '3.77342e-09', '1.10698e+05'], 'SSAgreement': '0.697'} [--------------------------------------------------------------------------------] 5 100.0 % 5 10 True UR1_1745_manA_cl4.pdb {'AnalyzeGeometry': 29.2553, 'eSCORE': 3.69212, 'FARNA': ['-77.776', '-17.102', '-49.686', '-292.441', '-41.381', '-708.309', '137.605', '313.606', '-76.946', '-779.964', '0.0', '0.0', '32.466', '0.0'], 'ClashScore': 157.221207, 'length': 188, 'SimRNA_0': ['0', '-1372.251842', '-632.170', '-142.165', '4.375', '-744.456972', '-58.938', '-154.305', '-96.999', '-67.785', '-366.430', '', '-1372.251842'], 'FARNA_hires': ['0.0', '-844.973', '-3.366', '0.0', '6.795', '24.541', '-645.037', '35.579', '-447.88', '2.991', '-288.621', '72.159', '-33.808', '406.525', '25.148'], 'RNAscore': 23.5789, 'RASP': ['2.2518', '2417', '0.000931651', '21.1599', '5.99801', '-3.15239', '-15114.4', '150933', '-0.10014', '-14522.8', '65.115', '-9.08602', '-33406.8', '340536', '-0.0981007', '-31563.6', '116.826', '-15.778', '-77213.4', '1168304', '-0.0660902', '0', '0', '0'], 'RNAkb': ['3.52283e+04', '3.42592e+04', '1.87299e+04', '8.69658e+01', '0.00000e+00', '0.00000e+00', '-2.06376e-03', '0.00000e+00', '8.83044e+04', '3.27448e-09', '8.83044e+04'], 'RNAkb_all': ['3.52283e+04', '3.42592e+04', '1.87299e+04', '8.69658e+01', '0.00000e+00', '0.00000e+00', '-1.90541e-03', '0.00000e+00', '8.83044e+04', '3.27448e-09', '8.83044e+04'], 'SSAgreement': '0.672'} Cmd: mqaprna.py -s /home/mqapRNA/mqapRNAweb/media/jobs/9f6a45f7-1d0e-4b83-b8d5-2ed1b2d4f8ab/ss.txt -m 6 -f -o /home/mqapRNA/mqapRNAweb/media/jobs/9f6a45f7-1d0e-4b83-b8d5-2ed1b2d4f8ab/9f6a45f_raw.csv input/UR1_1745_manA_cl1.pdb input/UR1_1745_manA_cl2.pdb input/UR1_1745_manA_cl3.pdb input/UR1_1745_manA_cl4.pdb input/UR1_1745_manA_cl5.pdb Execution time: 0:24:26.548 process: 6 start: 14:45:06 end: 15:09:33 Output: /home/mqapRNA/mqapRNAweb/media/jobs/9f6a45f7-1d0e-4b83-b8d5-2ed1b2d4f8ab/9f6a45f_raw.csv logging: /home/mqapRNA/mqapRNAweb/media/jobs/9f6a45f7-1d0e-4b83-b8d5-2ed1b2d4f8ab/9f6a45f_raw.log logging wrappers /home/mqapRNA/mqaprna_env/log/