mqaprna.py

ver: 52e618e-dirty

start  2017-10-06 16:16:44
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Seq ss fn                   /home/mqapRNA/mqapRNAweb/media/jobs/62d2e3ea-f7b4-4e56-b3f1-13f84c84c110/ss.txt
Output csv                  /home/mqapRNA/mqapRNAweb/media/jobs/62d2e3ea-f7b4-4e56-b3f1-13f84c84c110/62d2e3e_raw.csv
Input files                 #6 ['input/17_Bujnicki_7_rpr.pdb', 'input/17_Das_1_rpr.pdb', 'input/17_Das_4_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              CGUGGUUAGGGCCACGUUAAAUAGUUGCUUAAGCCCUAAGCGUUGAUAAAUAUCAGGUGCAA
 ref_ss               ((((.[[[[[[.))))........((((.....]]]]]]...(((((....)))))..))))
 to ignore 0 []
 files to analyze: 6 ['input/17_Bujnicki_7_rpr.pdb', 'input/17_Das_1_rpr.pdb', 'input/17_Das_4_rpr.pdb', 'input/17_Dohkolyan_1_rpr.pdb', 'input/17_Major_6_rpr.pdb']
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[-------------                                                                   ]      1 16.67 % 6 10
True 17_Das_4_rpr.pdb     {'AnalyzeGeometry': 22.5806, 'eSCORE': 1.43315, 'FARNA': ['-26.525', '-1.027', '-17.909', '-108.973', '-14.302', '-221.889', '13.636', '0.96', '-11.373', '-368.764', '0.0', '0.0', '18.638', '0.0'], 'ClashScore': 15.577889, 'length': 62, 'SimRNA_0': ['0', '-547.921961', '-298.538', '-84.436', '-1.117', '-248.266965', '-44.125', '-40.615', '-28.469', '-29.506', '-105.552', '', '-547.921961'], 'FARNA_hires': ['0.0', '-356.837', '-0.153', '0.0', '1.461', '4.543', '-314.55', '8.672', '-148.481', '2.224', '-90.612', '16.314', '-9.024', '168.925', '3.841'], 'RNAscore': 16.5026, 'RASP': ['-0.6548', '636', '-0.00102956', '6.8104', '3.46301', '-2.1557', '-5511.89', '39337', '-0.14012', '-5290.65', '42.323', '-5.22752', '-12670.2', '89379', '-0.141758', '-11933.4', '77.4955', '-9.5072', '-29371.8', '309432', '-0.0949216', '0', '0', '0'], 'RNAkb': ['5.98349e+03', '2.50340e+03', '5.66775e+03', '6.23377e-01', '0.00000e+00', '0.00000e+00', '-2.05920e-03', '0.00000e+00', '1.41553e+04', '9.50833e-10', '1.41553e+04'], 'RNAkb_all': ['5.98349e+03', '2.50340e+03', '5.66775e+03', '6.23377e-01', '0.00000e+00', '0.00000e+00', '-7.84210e-04', '0.00000e+00', '1.41553e+04', '9.50833e-10', '1.41553e+04'], 'SSAgreement': 'error'}
[--------------------------                                                      ]      2 33.33 % 6 10
True 17_Das_1_rpr.pdb     {'AnalyzeGeometry': 17.7419, 'eSCORE': 1.43655, 'FARNA': ['-25.941', '-0.781', '-20.339', '-102.772', '-15.772', '-210.313', '10.926', '0.849', '-13.508', '-357.486', '0.0', '0.0', '20.165', '0.0'], 'ClashScore': 8.542714, 'length': 62, 'SimRNA_0': ['0', '-577.595885', '-304.467', '-96.772', '-0.145', '-272.983295', '-49.021', '-47.144', '-32.107', '-35.486', '-109.226', '', '-577.595885'], 'FARNA_hires': ['0.0', '-359.206', '0.0', '0.0', '1.471', '5.196', '-305.984', '7.254', '-156.252', '2.305', '-87.686', '12.931', '-4.166', '162.618', '3.105'], 'RNAscore': 16.1099, 'RASP': ['-3.1964', '583', '-0.00548268', '4.77178', '2.36214', '-3.37328', '-5591.36', '36005', '-0.155294', '-5305.38', '32.8831', '-8.69686', '-12988.6', '81838', '-0.158711', '-12103.4', '73.5883', '-12.029', '-30282.5', '283765', '-0.106717', '0', '0', '0'], 'RNAkb': ['5.96636e+03', '2.50310e+03', '5.72950e+03', '6.46352e-01', '0.00000e+00', '0.00000e+00', '-1.54358e-03', '0.00000e+00', '1.41996e+04', '9.48439e-10', '1.41996e+04'], 'RNAkb_all': ['5.96636e+03', '2.50310e+03', '5.72950e+03', '6.46352e-01', '0.00000e+00', '0.00000e+00', '-7.57241e-04', '0.00000e+00', '1.41996e+04', '9.48439e-10', '1.41996e+04'], 'SSAgreement': 'error'}
[----------------------------------------                                        ]      3 50.0 % 6 10
True 17_Bujnicki_7_rpr.pdb {'AnalyzeGeometry': 11.2903, 'eSCORE': 1.40036, 'FARNA': ['-26.41', '-5.748', '-18.393', '-104.358', '-14.32', '-215.78', '7.509', '6.818', '-7.173', '-359.656', '0.0', '0.0', '18.198', '0.0'], 'ClashScore': 1.507538, 'length': 62, 'SimRNA_0': ['0', '-536.728354', '-283.215', '-80.145', '-0.846', '-252.667248', '-37.963', '-47.092', '-36.305', '-27.303', '-104.003', '', '-536.728354'], 'FARNA_hires': ['0.0', '-296.586', '-1.87', '0.0', '1.195', '7.668', '-272.229', '7.609', '-140.549', '2.357', '-78.84', '10.195', '-6.769', '171.206', '3.44'], 'RNAscore': 17.3346, 'RASP': ['-1.5117', '640', '-0.00236203', '7.41012', '3.72668', '-2.39404', '-5280.66', '38946', '-0.135589', '-5000.6', '38.2625', '-7.31958', '-11803.8', '88867', '-0.132825', '-10956.8', '79.3093', '-10.6789', '-26922.2', '300533', '-0.0895815', '0', '0', '0'], 'RNAkb': ['6.63748e+03', '4.08482e+03', '5.46709e+03', '1.25895e+00', '0.00000e+00', '0.00000e+00', '-1.04038e-03', '0.00000e+00', '1.61906e+04', '9.94050e-10', '1.61906e+04'], 'RNAkb_all': ['6.63748e+03', '4.08482e+03', '5.46709e+03', '1.25895e+00', '0.00000e+00', '0.00000e+00', '-7.12617e-04', '0.00000e+00', '1.61906e+04', '9.94050e-10', '1.61906e+04'], 'SSAgreement': 'error'}
[-----------------------------------------------------                           ]      4 66.67 % 6 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': 62, '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', '5.07149', '3.13486', '0.170504', '-5369.01', '37749', '-0.142229', '-5229.89', '34.8523', '-3.99167', '-12368.4', '88312', '-0.140053', '-11990.9', '65.0115', '-5.8056', '-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': 'error'}
[------------------------------------------------------------------              ]      5 83.33 % 6 10
True 5k7c_clean_onechain_renumber_as_puzzle_rpr.pdb {'AnalyzeGeometry': 18.9655, 'eSCORE': 1.18242, 'FARNA': ['-24.402', '-18.584', '-23.731', '-92.703', '-18.527', '-224.685', '20.866', '8.959', '-35.264', '-392.161', '0.0', '0.0', '15.91', '0.0'], 'ClashScore': 22.031166, 'length': 62, 'SimRNA_0': ['0', '-310.065637', '-230.308', '-68.038', '-3.207', '-76.550649', '119.627', '-46.804', '-30.228', '-20.818', '-98.328', '', '-310.065637'], 'FARNA_hires': ['0.0', '-406.345', '0.0', '0.0', '1.437', '6.281', '-362.292', '10.09', '-155.932', '2.326', '-90.583', '11.494', '-15.183', '180.695', '5.322'], 'RNAscore': 17.6751, 'RASP': ['-3.5107', '682', '-0.00514765', '4.72163', '3.71742', '-2.21452', '-4452.3', '41509', '-0.107261', '-4272.11', '44.1156', '-4.08462', '-10471.5', '94496', '-0.110814', '-9753.98', '77.0364', '-9.31428', '-23564.5', '330384', '-0.0713245', '0', '0', '0'], 'RNAkb': -1, 'RNAkb_all': -1, 'SSAgreement': 'error'}
[--------------------------------------------------------------------------------]      6 100.0 % 6 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': 62, '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', '-270.911', '-0.315', '0.0', '2.259', '7.679', '-233.986', '11.287', '-142.774', '3.988', '-88.829', '15.689', '-2.789', '126.992', '29.886'], 'RNAscore': 24.4173, 'RASP': ['2.993', '757', '0.00395376', '5.95724', '3.28124', '-0.903391', '-2982.08', '44679', '-0.0667446', '-2941.63', '38.5309', '-1.04971', '-6128.49', '104153', '-0.0588412', '-6089.17', '79.392', '-0.495189', '-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': 'error'}

Cmd: mqaprna.py -s /home/mqapRNA/mqapRNAweb/media/jobs/62d2e3ea-f7b4-4e56-b3f1-13f84c84c110/ss.txt -m 6 -f -o /home/mqapRNA/mqapRNAweb/media/jobs/62d2e3ea-f7b4-4e56-b3f1-13f84c84c110/62d2e3e_raw.csv input/17_Bujnicki_7_rpr.pdb input/17_Das_1_rpr.pdb input/17_Das_4_rpr.pdb input/17_Dohkolyan_1_rpr.pdb input/17_Major_6_rpr.pdb input/5k7c_clean_onechain_renumber_as_puzzle_rpr.pdb
Execution time: 0:03:34.636 process: 6 start: 16:16:44 end: 16:20:19  
Output: /home/mqapRNA/mqapRNAweb/media/jobs/62d2e3ea-f7b4-4e56-b3f1-13f84c84c110/62d2e3e_raw.csv 

logging: /home/mqapRNA/mqapRNAweb/media/jobs/62d2e3ea-f7b4-4e56-b3f1-13f84c84c110/62d2e3e_raw.log
logging wrappers /home/mqapRNA/mqaprna_env/log/