mqaprna.py

ver: 981a817-dirty

start  2017-07-05 12:41:03
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Seq ss fn                   /home/mqapRNA/mqapRNAweb/media/jobs/df925749-58e8-4f00-bbe3-bbd8b6590a6a/ss.txt
Output csv                  /home/mqapRNA/mqapRNAweb/media/jobs/df925749-58e8-4f00-bbe3-bbd8b6590a6a/df92574_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                     SimRNA_0
rmsd                        biopython_all
Native pdb                  off
RASP                        all
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AnalyzeGeometry             on
SSAgreement                 on
 pdb_id               >seq
 ref_seq              
 ref_ss               ..((.(((((((....................))))))).))(((((....)))))......
 to ignore 0 []
 files to analyze: 1 ['input/17_Major_6_rpr.pdb']
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[--------------------------------------------------------------------------------]      1 100.0 % 1 10
True 17_Major_6_rpr.pdb   {'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']}

Cmd: mqaprna.py -t SimRNA_0 -s /home/mqapRNA/mqapRNAweb/media/jobs/df925749-58e8-4f00-bbe3-bbd8b6590a6a/ss.txt -m 6 -f -o /home/mqapRNA/mqapRNAweb/media/jobs/df925749-58e8-4f00-bbe3-bbd8b6590a6a/df92574_raw.csv input/17_Major_6_rpr.pdb
Execution time: 0:00:00.651 process: 6 start: 12:41:03 end: 12:41:03  
Output: /home/mqapRNA/mqapRNAweb/media/jobs/df925749-58e8-4f00-bbe3-bbd8b6590a6a/df92574_raw.csv 

logging: /home/mqapRNA/mqapRNAweb/media/jobs/df925749-58e8-4f00-bbe3-bbd8b6590a6a/df92574_raw.log
logging wrappers /home/mqapRNA/mqaprna_env/log/
in: /home/mqapRNA/mqapRNAweb/media/jobs/df925749-58e8-4f00-bbe3-bbd8b6590a6a/df92574_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.
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H2O cluster uptime:         14 days 5 hours 13 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
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Parse progress: [#########################################################] 100%
deeplearning prediction progress: [#######################################] 100%
deeplearning prediction progress: [#######################################] 100%
  mqapRNA
---------
  3.01662

[1 row x 1 column]

fn
------------------
17_Major_6_rpr.pdb

[1 row x 1 column]

Exporting to  /home/mqapRNA/mqapRNAweb/media/jobs/df925749-58e8-4f00-bbe3-bbd8b6590a6a/df92574_raw_mqapRNA.csv
Export File progress: [###################################################] 100%
                    simrna_steps  simrna_total_energy  simrna_base_base  \
fn                                                                        
17_Major_6_rpr.pdb             0          -213.643135           -82.771   

                    simrna_short_stacking  simrna_base_backbone  \
fn                                                                
17_Major_6_rpr.pdb                -17.374                 0.912   

                    simrna_local_geometry  simrna_bonds_dist_cp  \
fn                                                                
17_Major_6_rpr.pdb            -131.784132               -36.482   

                    simrna_bonds_dist_pc  simrna_flat_angles_cpc  \
fn                                                                 
17_Major_6_rpr.pdb               -36.334                 -28.376   

                    simrna_flat_angles_pcp  simrna_tors_eta_theta  \
fn                                                                  
17_Major_6_rpr.pdb                   4.459                -35.051   

                    simrna_sphere_penalty  simrna_chain_energy   mqapRNA  
fn                                                                        
17_Major_6_rpr.pdb                    NaN          -213.643135  3.016623  
                     mqapRNA
fn                          
17_Major_6_rpr.pdb  3.016623
  saved  /home/mqapRNA/mqapRNAweb/media/jobs/df925749-58e8-4f00-bbe3-bbd8b6590a6a/df92574_mqapRNA.csv
H2O session _sid_93a0 closed.