Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  4% [===                                               ] -                     
  9% [=====                                             ] \                     
 14% [========                                          ] |                     
 19% [==========                                        ] /                     
 24% [=============                                     ] -                     
 29% [===============                                   ] \                     
 34% [==================                                ] |                     
 39% [====================                              ] /                     
 44% [=======================                           ] -                     
 49% [=========================                         ] \                     
 54% [============================                      ] |                     
 59% [==============================                    ] /                     
 64% [=================================                 ] -                     
 69% [===================================               ] \                     
 74% [======================================            ] |                     
 79% [========================================          ] /                     
 84% [===========================================       ] -                     
 89% [=============================================     ] \                     
 94% [================================================  ] |                     
 99% [==================================================] /                     done.
Writing output ct file...done.
Single strand folding complete.
Initializing nucleic acids...done.
Applying SHAPE constraints...done.
Calculating free energies...done.
efn2 complete.
Converting CT file...CT file conversion complete.
/disk1/www/rails/humanrnamap/cli/./main.py:567: DeprecationWarning: Call to deprecated function (or staticmethod) VARNA. (Class has been renamed 'Structure')
  v = VARNA(structure=fold_dbn, sequence=seq)
Output file: /disk1/www/rails/humanrnamap/public/result/f3cab288-f715-4aa5-8202-f68be02dd061/final_image/NFKB1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.23 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.23 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.23 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.89 MB
Based on canonical annotations, the following gene is in your area of interest: NFKB1(+)
write fasta - Elapsed time since the previous call: 0.36 seconds
write fasta - Current memory usage: 172.89 MB
Length of region: 101 nt.
100.0% of the region's A/C bases included in the filtered DMS dataset. Ideally, this number should be as high as possible for an experimenally-accurate prediction, and over 70% is recommended.
write dat - Elapsed time since the previous call: 0.18 seconds
write dat - Current memory usage: 176.45 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/f3cab288-f715-4aa5-8202-f68be02dd061/fasta/NFKB1.fasta" "/disk1/www/rails/humanrnamap/public/result/f3cab288-f715-4aa5-8202-f68be02dd061/ct/NFKB1.ct" --SHAPE "NFKB1.dat"

fold - Elapsed time since the previous call: 0.13 seconds
fold - Current memory usage: 176.45 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/f3cab288-f715-4aa5-8202-f68be02dd061/ct/NFKB1.ct" "/disk1/www/rails/humanrnamap/public/result/f3cab288-f715-4aa5-8202-f68be02dd061/fold_FE/NFKB1.txt" -sh "NFKB1.dat"

efn2 - Elapsed time since the previous call: 0.50 seconds
efn2 - Current memory usage: 176.45 MB
This region has 1 predicted structures. 5 is the maximum structures visible on the web server. For up to 20 predictions per region, download and run the code locally.
Running command: /disk1/www/rails/humanrnamap/cli/bin/ct2dot "/disk1/www/rails/humanrnamap/public/result/f3cab288-f715-4aa5-8202-f68be02dd061/ct/NFKB1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/f3cab288-f715-4aa5-8202-f68be02dd061/fold_dbn/NFKB1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.45 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'ACAGCUGGCUGAAGAUGUGAAGCUGCAGCUGUAUAAGUUACUAGAAAUUCCUGAUCCAGACAAAAACUGGGCUACUCUGGCGCAGAAAUUAGGUCUGGGGA', '-structureDBN', '((((((((((..........)))..)))))))......................(((((((.....(((.(((.....))).))).......)))))))..', '-o', '/disk1/www/rails/humanrnamap/public/result/f3cab288-f715-4aa5-8202-f68be02dd061/final_image/NFKB1_fold_1.svg', '-title', 'NFKB1, -33.8 ± 1.0\n kcal/mol, AUC: 0.836', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '4,6,7,8,10,11,14,16,17,18,19,22,24,25,28,30,31,32,34,37,38,39,42,44,48,49,52,53,55,59,68,69,70,71,73,76,78,79,80,82,85,89,90,92,93,94,96,97,98,99,100', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '3,58,5,9,13,45,81,83,86,57,26,27', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,2,66,40,84,54,23,56,60,29,62', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,65,67,72,74,75,12,77,15,20,21,87,88,91,95,33,35,36,101,41,43,46,47,50,51,61,63']
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 87.4280673455716, Y: 366.11302763445406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 87.4280673455716, Y: 346.11302763445406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 87.4280673455716, Y: 326.11302763445406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 87.4280673455716, Y: 306.11302763445406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 87.4280673455716, Y: 286.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 87.4280673455716, Y: 266.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 87.4280673455716, Y: 246.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 80.74975065224862, Y: 229.99014489961115, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 66.60761502851767, Y: 215.8480092758802, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 52.46547940478672, Y: 201.70587365214925, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 35.01859038300597, Y: 203.06792217190957, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 18.961410152949213, Y: 196.10975605086975, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 8.02483926689473, Y: 182.44811156849426, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 4.75, Y: 165.25728434917409, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 9.897804259239138, Y: 148.53157886279553, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 22.272155003995692, Y: 136.15722811803897, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 38.997860490374194, Y: 131.00942385879978, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 56.18868770969442, Y: 134.2842631256945, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 69.85033219206991, Y: 145.22083401174888, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 76.8084983131098, Y: 161.2780142418057, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 75.44644979334953, Y: 178.72490326358644, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 89.58858541708048, Y: 192.8670388873174, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 103.73072104081143, Y: 207.00917451104834, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 119.90328416563074, Y: 213.737095593677, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 126.60643777948422, Y: 229.91993995891227, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 119.9280673455716, Y: 246.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 119.9280673455716, Y: 266.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 119.9280673455716, Y: 286.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 119.9280673455716, Y: 306.11302763445406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 119.9280673455716, Y: 326.11302763445406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 119.9280673455716, Y: 346.11302763445406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 119.9280673455716, Y: 366.11302763445406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 137.4280673455716, Y: 366.11302763445406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 154.9280673455716, Y: 366.11302763445406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 172.4280673455716, Y: 366.11302763445406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 189.9280673455716, Y: 366.11302763445406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 207.4280673455716, Y: 366.11302763445406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 224.9280673455716, Y: 366.11302763445406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 242.4280673455716, Y: 366.11302763445406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 259.9280673455716, Y: 366.11302763445406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 277.4280673455716, Y: 366.11302763445406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 294.9280673455716, Y: 366.11302763445406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 312.4280673455716, Y: 366.11302763445406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 329.9280673455716, Y: 366.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 347.4280673455716, Y: 366.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 364.9280673455716, Y: 366.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 382.4280673455716, Y: 366.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 399.9280673455716, Y: 366.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 417.4280673455716, Y: 366.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 434.9280673455716, Y: 366.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 452.4280673455716, Y: 366.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 469.9280673455716, Y: 366.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 487.4280673455716, Y: 366.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 504.92806734557166, Y: 366.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 522.4280673455717, Y: 366.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 522.4280673455717, Y: 346.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 522.4280673455717, Y: 326.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 522.4280673455717, Y: 306.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 522.4280673455717, Y: 286.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 522.4280673455717, Y: 266.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 522.4280673455717, Y: 246.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 507.15240391746715, Y: 237.57465660870253, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 495.7798103021173, Y: 224.27376237552306, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 489.71828309677153, Y: 207.8570769341506, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 489.71827641664055, Y: 190.35708627866512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 495.7797910887655, Y: 173.94039620966117, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 507.1523745496247, Y: 160.63949329414783, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 500.2249040254567, Y: 141.87755970145054, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 493.29743350128854, Y: 123.11562610875325, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 481.4297063953586, Y: 110.25465982707743, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 482.0918448635487, Y: 92.76726513809729, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 475.1643085844008, Y: 74.00535582424845, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 468.23677230525294, Y: 55.24344651039951, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 456.39299272061066, Y: 42.360291113212156, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 457.1068456734643, Y: 24.874833675690866, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 469.96138312186525, Y: 13.0, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 487.4485122606492, Y: 13.671656401116707, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 499.3543308784831, Y: 26.497501046866432, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 498.72487494025745, Y: 43.98620005678413, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 505.6524112194053, Y: 62.748109370633074, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 512.5799474985531, Y: 81.5100186844819, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 524.447747512151, Y: 94.37101875590906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 523.7855755894216, Y: 111.85848650698011, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 530.7130461135896, Y: 130.6204200996774, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 537.6405166377579, Y: 149.3823536923747, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 554.9280404307544, Y: 152.10108889584257, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 570.2037160897479, Y: 160.63945719202383, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 581.5763195856839, Y: 173.94035527163572, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 587.6378515943717, Y: 190.35704890061152, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 587.6378566044726, Y: 207.85704890061083, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 581.576333995705, Y: 224.27374600031385, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 570.2037381156384, Y: 237.57465059168254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 554.9280673455717, Y: 246.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 554.9280673455717, Y: 266.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 554.9280673455717, Y: 286.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 554.9280673455717, Y: 306.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 554.9280673455717, Y: 326.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 554.9280673455717, Y: 346.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 554.9280673455717, Y: 366.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 572.4280673455717, Y: 366.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 589.9280673455717, Y: 366.1130276344541, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 88.1780673455716, Y: 386.11302763445406, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 39.56072210731653, Y: 219.48761762804813, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 92.7852196989088, Y: 157.9830994679367, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 136.1780673455716, Y: 326.11302763445406, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 256.1780673455716, Y: 386.11302763445406, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 431.1780673455716, Y: 386.1130276344541, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 498.67806734557166, Y: 266.1130276344541, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 458.91778494205676, Y: 117.1821632287461, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 520.6643205332541, Y: 55.82057309148513, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '90', X: 603.5759092064412, Y: 211.37565441162204, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '100', X: 564.1780673455717, Y: 386.1130276344541, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '101', X: 581.6780673455717, Y: 386.1130276344541, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'NFKB1, -33.8 ± 1.0
 kcal/mol, AUC: 0.836', X: 231.33903367278583, Y: 398.9130276344541, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 621.5759092064412, 398.9130276344541)
Updated viewBox: -0.25 0.0 626.8259092064412 403.9130276344541
Updated SVG: /disk1/www/rails/humanrnamap/public/result/f3cab288-f715-4aa5-8202-f68be02dd061/final_image/NFKB1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/f3cab288-f715-4aa5-8202-f68be02dd061/final_image/NFKB1_fold_final_1.svg
