Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  6% [====                                              ] -                     
 12% [=======                                           ] \                     
 18% [==========                                        ] |                     
 25% [=============                                     ] /                     
 31% [================                                  ] -                     
 37% [===================                               ] \                     
 43% [======================                            ] |                     
 50% [==========================                        ] /                     
 56% [=============================                     ] -                     
 62% [================================                  ] \                     
 68% [===================================               ] |                     
 75% [======================================            ] /                     
 81% [=========================================         ] -                     
 87% [============================================      ] \                     
 93% [===============================================   ] |                     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/cea40566-1b3e-4c93-b061-2cdfd73d93fd/final_image/NFKB1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.58 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.58 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.58 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.20 MB
Based on canonical annotations, the following gene is in your area of interest: NFKB1(+)
write fasta - Elapsed time since the previous call: 0.34 seconds
write fasta - Current memory usage: 172.20 MB
Length of region: 80 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: 0.24 seconds
write dat - Current memory usage: 175.76 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/cea40566-1b3e-4c93-b061-2cdfd73d93fd/fasta/NFKB1.fasta" "/disk1/www/rails/humanrnamap/public/result/cea40566-1b3e-4c93-b061-2cdfd73d93fd/ct/NFKB1.ct" --SHAPE "NFKB1.dat"

fold - Elapsed time since the previous call: 0.09 seconds
fold - Current memory usage: 175.76 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/cea40566-1b3e-4c93-b061-2cdfd73d93fd/ct/NFKB1.ct" "/disk1/www/rails/humanrnamap/public/result/cea40566-1b3e-4c93-b061-2cdfd73d93fd/fold_FE/NFKB1.txt" -sh "NFKB1.dat"

efn2 - Elapsed time since the previous call: 0.51 seconds
efn2 - Current memory usage: 175.76 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/cea40566-1b3e-4c93-b061-2cdfd73d93fd/ct/NFKB1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/cea40566-1b3e-4c93-b061-2cdfd73d93fd/fold_dbn/NFKB1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.76 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CUAGAAGGCAAAAUUUAGCCUGCUGACAAUUUCCCACACCGUGUAAACCAAAGCCCUAAAAUUCCACUGCGUUGUCCACA', '-structureDBN', '.(((.((((........)))).)))...............(((...(.(((.((..............)).)))).))).', '-o', '/disk1/www/rails/humanrnamap/public/result/cea40566-1b3e-4c93-b061-2cdfd73d93fd/final_image/NFKB1_fold_1.svg', '-title', 'NFKB1, -9.2 ± 0.7\n kcal/mol, AUC: 0.619', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,4,68,69,7,8,71,72,73,74,75,14,15,16,18,21,22,24,25,30,31,32,41,42,43,44,53,57,62,63', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '36,38,11,77,51,20,56,59,60,61', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '64,67,6,70,9,10,76,80,17,19,26,33,34,46,47,48,49,50,54,58', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,65,3,66,5,12,13,78,79,23,27,28,29,35,37,39,40,45,52,55']
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 11.98829605080223, Y: 229.015317232598, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 29.488296050802234, Y: 229.015317232598, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 29.488296050802234, Y: 209.015317232598, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 29.488296050802234, Y: 189.015317232598, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 22.809918899312972, Y: 172.83978080251524, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 29.488296050802234, Y: 156.66424437243248, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 29.488296050802234, Y: 136.66424437243245, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 29.488296050802205, Y: 116.66424437243245, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 29.488296050802205, Y: 96.66424437243248, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 17.833227976518483, Y: 83.61013018425234, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 15.150085360253879, Y: 66.31703171246255, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 22.301541444097577, Y: 50.34495655188658, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 36.988288778601884, Y: 40.82918218577936, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 54.4883033230025, Y: 40.8291821857793, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 69.17505065750683, Y: 50.34495655188658, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 76.32650674135047, Y: 66.31703171246255, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 73.64336412508592, Y: 83.61013018425234, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 61.988296050802205, Y: 96.66424437243248, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 61.988296050802205, Y: 116.66424437243245, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 61.988296050802234, Y: 136.66424437243245, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 61.988296050802234, Y: 156.66424437243245, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 68.66667320229149, Y: 172.83978080251524, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 61.988296050802234, Y: 189.015317232598, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 61.988296050802234, Y: 209.015317232598, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 61.988296050802234, Y: 229.015317232598, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 79.48829605080223, Y: 229.015317232598, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 96.98829605080223, Y: 229.015317232598, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 114.48829605080223, Y: 229.015317232598, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 131.98829605080223, Y: 229.01531723259802, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 149.48829605080223, Y: 229.01531723259802, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 166.98829605080223, Y: 229.01531723259802, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 184.48829605080223, Y: 229.01531723259802, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 201.98829605080223, Y: 229.01531723259802, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 219.48829605080223, Y: 229.01531723259802, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 236.98829605080223, Y: 229.01531723259802, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 254.4882960508022, Y: 229.01531723259802, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 271.9882960508022, Y: 229.01531723259802, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 289.4882960508022, Y: 229.01531723259802, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 306.9882960508022, Y: 229.01531723259802, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 324.4882960508022, Y: 229.01531723259802, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 341.9882960508022, Y: 229.01531723259802, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 341.9882960508022, Y: 209.01531723259802, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 341.9882960508022, Y: 189.01531723259802, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 331.6086121544624, Y: 174.92587624953146, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 331.6086138912769, Y: 157.42587096372517, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 341.9883005842722, Y: 143.33643204095372, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 358.7018906438767, Y: 138.14932375957557, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 365.75989402659934, Y: 122.13567776383815, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 382.59545147523414, Y: 117.35903927835108, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 400.18285985140204, Y: 107.83627357662874, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 417.77026822756994, Y: 98.31350787490646, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 428.81469009663, Y: 84.73896751666771, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 446.21876764356284, Y: 82.90990078754788, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 463.80614264514844, Y: 73.38707344722485, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 464.5145664636476, Y: 55.9014223959943, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 471.532129819175, Y: 39.87008865412571, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 483.89825030552714, Y: 27.487483067697724, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 499.9202210427833, Y: 20.448569040198606, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 517.4049128173978, Y: 19.716851513591962, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 533.9589753387238, Y: 25.392489894606342, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 547.3164452796684, Y: 36.698587973465294, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 555.6489172569646, Y: 52.08753750680211, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 557.8158207369288, Y: 69.45285887729608, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 553.5205443099675, Y: 86.41754152708373, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 543.3510366352499, Y: 100.65941537310127, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 528.6993264921659, Y: 110.22901551496022, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 511.57097824418554, Y: 113.81643008368818, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 494.3105649490461, Y: 110.93060440063181, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 479.2807370731734, Y: 101.9665578248013, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 461.69336207158784, Y: 111.48938516512436, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 450.6489171137533, Y: 125.06400249208292, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 433.2447624928687, Y: 126.89304648617934, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 415.6573541167008, Y: 136.41581218790162, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 398.0699457405329, Y: 145.93857788962393, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 384.86798168395546, Y: 157.42588153533808, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 384.8679782103275, Y: 174.92588153533774, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 374.4882960508022, Y: 189.01531723259802, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 374.4882960508022, Y: 209.01531723259802, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 374.4882960508022, Y: 229.01531723259802, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 391.9882960508022, Y: 229.01531723259802, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 12.73829605080223, Y: 249.015317232598, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: -4.0, Y: 92.15395052115429, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 78.23829605080223, Y: 136.66424437243245, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 145.73829605080223, Y: 249.01531723259802, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 320.7382960508022, Y: 249.01531723259802, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 386.91009414967976, Y: 90.24886520046081, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 540.0832497559161, Y: 8.0, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 467.4661740022714, Y: 129.0767685103759, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 388.2382960508022, Y: 249.01531723259802, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'NFKB1, -9.2 ± 0.7
 kcal/mol, AUC: 0.619', X: 218.9020583938655, Y: 261.81531723259803, Width: 142.5, Height: 23
Calculated bounding box: (-4.0, 0.0, 568.3158207369288, 261.81531723259803)
Updated viewBox: -9.0 -5.0 582.3158207369288 271.81531723259803
Updated SVG: /disk1/www/rails/humanrnamap/public/result/cea40566-1b3e-4c93-b061-2cdfd73d93fd/final_image/NFKB1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/cea40566-1b3e-4c93-b061-2cdfd73d93fd/final_image/NFKB1_fold_final_1.svg
