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                            NeEDL                              
  Scalable network-based epistasis detection via local search  
                          version 1.0                          
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[23/02/27-18:03:17.450124]  parameters:
[23/02/27-18:03:17.450177]      ./test/model/bin/NeEDL 
[23/02/27-18:03:17.450208]      --num-threads 20 
[23/02/27-18:03:17.450238]      --input-path /nfs/proj/GenEpiSeeker/tools_juli/datasets/current/BD_MHASDC/dataset.json 
[23/02/27-18:03:17.450267]      --input-format JSON_EPIGEN 
[23/02/27-18:03:17.450294]      --phenotype CATEGORICAL 
[23/02/27-18:03:17.450323]      --num-categories 2 
[23/02/27-18:03:17.450352]      --output-directory /nfs/proj/GenEpiSeeker/tools_juli/NeEDL/NeEDL_runs/results_prod2 
[23/02/27-18:03:17.450380]      --snp-annotate-dbSNP 
[23/02/27-18:03:17.450408]      --network-BIOGRID 
[23/02/27-18:03:17.450436]      --ms-model PENETRANCE 
[23/02/27-18:03:17.450464]      --ms-seeding-routine RANDOM_CONNECTED 
[23/02/27-18:03:17.450493]      --ms-rc-start-seeds 5000 
[23/02/27-18:03:17.450521]      --ms-search-time-limit 3d 
[23/02/27-18:03:17.450549]      --disable-final-search 
[23/02/27-18:03:17.450578]  Log file: /nfs/proj/GenEpiSeeker/tools_juli/NeEDL/NeEDL_runs/results_prod2/23_02_27-18_03_17-8348199100156678072/run.log
[23/02/27-18:03:17.450606]  OpenMP threads: 20 available, 20 selected
[23/02/27-18:03:17.699655]  Sequential pipeline 1 of 5
[23/02/27-18:03:17.699691]  Begin loading GWAS data
[23/02/27-18:03:17.699722]  input file: /nfs/proj/GenEpiSeeker/tools_juli/datasets/current/BD_MHASDC/dataset.json
[23/02/27-18:05:02.551671]  Finished loading GWAS data in 104.850197 sec
[23/02/27-18:05:02.551737]  Sequential pipeline 2 of 5
[23/02/27-18:05:02.551770]  Begin annotating SNPs with CSV map
[23/02/27-18:05:22.016006]  Finished annotating SNPs with CSV map in 19.462072 sec
[23/02/27-18:05:22.159172]  Sequential pipeline 3 of 5
[23/02/27-18:05:22.159186]  Begin connecting items with same label
[23/02/27-18:05:23.657682]  Finished connecting items with same label in 1.498436 sec
[23/02/27-18:05:23.664778]  Sequential pipeline 4 of 5
[23/02/27-18:05:23.664790]  network stats: 
[23/02/27-18:05:23.664839]      nodes:                140318
[23/02/27-18:05:23.664847]      edges:                5084530
[23/02/27-18:05:23.664899]      % of possible edges:  0.0516484310 %
[23/02/27-18:05:23.701385]      annotations:          13085
[23/02/27-18:05:23.703159]  Sequential pipeline 5 of 5
[23/02/27-18:05:24.404325]  Multi-Network pipeline BIOGRID 1 of 1
[23/02/27-18:05:24.812739]  Sequential pipeline 1 of 8
[23/02/27-18:05:24.812755]  Begin connecting SNPs with CSV map BIOGRID
[23/02/27-18:05:41.920795]  Finished connecting SNPs with CSV map BIOGRID in 17.107975 sec
[23/02/27-18:05:42.088057]  Sequential pipeline 2 of 8
[23/02/27-18:05:42.088071]  network stats: 
[23/02/27-18:05:42.088079]      nodes:                142441
[23/02/27-18:05:42.088087]      edges:                26471155
[23/02/27-18:05:42.088112]      % of possible edges:  0.2609371459 %
[23/02/27-18:05:42.132670]      annotations:          15517
[23/02/27-18:05:42.139384]  Sequential pipeline 3 of 8
[23/02/27-18:05:42.139396]  Begin seeding with method RANDOM_CONNECTED
[23/02/27-18:05:42.579729]  Finished seeding with method RANDOM_CONNECTED in 0.440283 sec
[23/02/27-18:05:42.581271]  Sequential pipeline 4 of 8
[23/02/27-18:05:42.581281]  Begin saving network
[23/02/27-18:06:50.095983]  Finished saving network in 67.464691 sec
[23/02/27-18:06:50.096049]  Sequential pipeline 5 of 8
[23/02/27-18:06:50.096083]  Begin writing sets (+ calculating additional scores)
[23/02/27-18:09:40.204344]  Finished writing sets (+ calculating additional scores) in 2.835134 min
[23/02/27-18:09:40.205306]  Sequential pipeline 6 of 8
[23/02/27-18:09:40.205340]  Begin local search with time limit 4320.0000000000 min
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[23/02/27-20:01:53.777963]  Local search running: 4966 of 5000 start points done. Current best score is 1505.9432308979
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[23/02/27-20:02:29.994188]  Local search running: 4993 of 5000 start points done. Current best score is 1505.9432308979
[23/02/27-20:03:04.503175]  Local search running: 4996 of 5000 start points done. Current best score is 1505.9432308979
[23/02/27-20:03:14.681094]  Local search running: 4997 of 5000 start points done. Current best score is 1505.9432308979
[23/02/27-20:03:40.922473]  Local search running: 4998 of 5000 start points done. Current best score is 1505.9432308979
[23/02/27-20:04:08.574775]  Local search running: 4999 of 5000 start points done. Current best score is 1505.9432308979
[23/02/27-20:04:35.909255]  Local search running: 5000 of 5000 start points done. Current best score is 1505.9432308979
[23/02/27-20:04:35.909499]  Runs skipped due to exceeded search time limit: 0
[23/02/27-20:04:35.967935]  Finished local search with time limit 4320.0000000000 min in 114.929367 min
[23/02/27-20:04:35.972849]  Sequential pipeline 7 of 8
[23/02/27-20:04:35.972862]  Begin writing sets (+ calculating additional scores)
[23/02/27-20:06:25.113088]  Finished writing sets (+ calculating additional scores) in 109.140175 sec
[23/02/27-20:06:25.113336]  Sequential pipeline 8 of 8
[23/02/27-20:06:25.113348]  Begin writing individual SNPs (+ calculating additional scores)
[23/02/27-20:08:52.199299]  Finished writing individual SNPs (+ calculating additional scores) in 2.451432 min
[23/02/27-20:08:52.627056]  Construct new network from the preliminary results
[23/02/27-20:08:57.666872]  NeEDL-Pipeline finished successfully.
[23/02/27-20:08:57.666893]  RUN STATS: 
[23/02/27-20:08:57.666912]      User time (seconds): 143903.477043
[23/02/27-20:08:57.666921]      System time (seconds): 31.931151
[23/02/27-20:08:57.666931]      Elapsed (wall clock) time (seconds): 7540.358312
[23/02/27-20:08:57.666940]      Percent CPU this job got: 1908.866956%
[23/02/27-20:08:57.666949]      Maximum resident set size (kbytes): 10494188
[23/02/27-20:08:57.666957]      Major (requiring I/O) page faults: 354
[23/02/27-20:08:57.666966]      Minor (reclaiming a frame) page faults: 19446014
[23/02/27-20:08:57.666974]      Voluntary context switches: 111680
[23/02/27-20:08:57.666982]      Involuntary context switches: 98935
[23/02/27-20:08:57.666990]      File system inputs: 2218736
[23/02/27-20:08:57.666999]      File system outputs: 2024768
