Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  6% [====                                              ] -                     
 12% [=======                                           ] \                     
 18% [==========                                        ] |                     
 24% [=============                                     ] /                     
 30% [================                                  ] -                     
 36% [===================                               ] \                     
 42% [======================                            ] |                     
 48% [=========================                         ] /                     
 54% [============================                      ] -                     
 60% [===============================                   ] \                     
 66% [==================================                ] |                     
 72% [=====================================             ] /                     
 78% [========================================          ] -                     
 84% [===========================================       ] \                     
 90% [==============================================    ] |                     
 96% [================================================= ] /                     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/de354a6a-2964-45d7-a8ac-59d6bc7b61cd/final_image/BCOR_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.45 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.45 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.45 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.09 MB
Based on canonical annotations, the following gene is in your area of interest: BCOR(-)
write fasta - Elapsed time since the previous call: 0.26 seconds
write fasta - Current memory usage: 172.09 MB
Length of region: 83 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: 0.19 seconds
write dat - Current memory usage: 175.23 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/de354a6a-2964-45d7-a8ac-59d6bc7b61cd/fasta/BCOR.fasta" "/disk1/www/rails/humanrnamap/public/result/de354a6a-2964-45d7-a8ac-59d6bc7b61cd/ct/BCOR.ct" --SHAPE "BCOR.dat"

fold - Elapsed time since the previous call: 0.09 seconds
fold - Current memory usage: 175.23 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/de354a6a-2964-45d7-a8ac-59d6bc7b61cd/ct/BCOR.ct" "/disk1/www/rails/humanrnamap/public/result/de354a6a-2964-45d7-a8ac-59d6bc7b61cd/fold_FE/BCOR.txt" -sh "BCOR.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 175.23 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/de354a6a-2964-45d7-a8ac-59d6bc7b61cd/ct/BCOR.ct" 1 "/disk1/www/rails/humanrnamap/public/result/de354a6a-2964-45d7-a8ac-59d6bc7b61cd/fold_dbn/BCOR_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.23 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AGACUCCGAGAUGUGCAAAUUCAGCCCAGCCGACUGGGAAAGGUUGAAAGGAAAUCAGGACAAAAAGCCAAAGUCGGUCACCC', '-structureDBN', '....(((..(((...(((......(((((....))))).....))).......))).)))......(((......))).....', '-o', '/disk1/www/rails/humanrnamap/public/result/de354a6a-2964-45d7-a8ac-59d6bc7b61cd/final_image/BCOR_fold_1.svg', '-title', 'BCOR, -17.9 ± 1.2\n kcal/mol, AUC: 0.778', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,5,8,10,12,13,14,15,20,21,24,29,32,35,36,37,38,42,43,44,45,46,50,51,55,58,59,67,73,74,76,77,78', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '34,4,69,7,11,16,17,82,52,25,26,27,60,62', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '64,33,6,39,70,71,75,81,83,53,54,28,31', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,65,3,66,68,72,9,79,80,18,19,22,23,30,40,41,47,48,49,56,57,61,63']
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 7.963254636257588, Y: 432.06113334316535, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 25.463254636257588, Y: 432.06113334316535, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 42.96325463625759, Y: 432.06113334316535, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 60.46325463625759, Y: 432.06113334316535, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 77.96325463625759, Y: 432.06113334316535, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 77.96325463625759, Y: 412.06113334316535, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 77.96325463625759, Y: 392.06113334316535, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 69.16611960851222, Y: 376.93305688540175, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 72.22282102402899, Y: 359.7021295027939, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 85.68674079274345, Y: 348.5230800588588, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 92.56610021650042, Y: 329.7434524289305, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 99.44545964025738, Y: 310.9638247990022, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 88.93275514297314, Y: 296.97325270068626, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 84.66787149038406, Y: 280.00080942002455, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 87.31823813875079, Y: 262.7025834961148, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 96.46908814128055, Y: 247.78564655461776, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 87.85467119379831, Y: 229.73594238377518, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 79.24025424631607, Y: 211.68623821293266, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 61.81955639040085, Y: 210.02279886663143, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 46.216013115594976, Y: 202.0995936113593, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 34.59435342541305, Y: 189.0158338194832, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 28.566886995756292, Y: 172.58667094716156, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 28.969823344437046, Y: 155.09137482092171, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 35.74726183496536, Y: 138.9571233120039, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 47.958946948989094, Y: 126.42227225896602, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 42.856633240071844, Y: 107.08406151402392, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 37.75431953115462, Y: 87.74585076908181, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 32.65200582223737, Y: 68.40764002413971, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 27.54969211332012, Y: 49.06942927919761, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 19.74660761292988, Y: 33.405358164817585, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 26.967505366721284, Y: 17.464533618205337, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 43.888474345136856, Y: 13.0, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 58.033817419286095, Y: 23.303422776495495, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 58.97428457385108, Y: 40.778169502207106, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 64.07659828276833, Y: 60.11638024714921, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 69.17891199168557, Y: 79.45459099209131, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 74.2812257006028, Y: 98.79280173703341, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 79.38353940952005, Y: 118.13101248197552, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 96.18975688076308, Y: 123.00964490400588, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 110.04482036831412, Y: 133.70016480511129, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 119.02655885199412, Y: 148.71943155854444, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 121.8888981121023, Y: 165.9837593462123, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 118.23473382785049, Y: 183.0979956243434, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 108.57102352393521, Y: 197.68781067327404, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 117.18544047141744, Y: 215.73751484411662, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 125.7998574188997, Y: 233.78721901495913, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 143.152282732429, Y: 236.0551113709555, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 158.26751093448587, Y: 244.87440138771672, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 168.7801204926228, Y: 258.8649353402923, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 173.04496568501423, Y: 275.83729803630297, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 170.39462975051163, Y: 293.1354401167197, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 161.2438706804524, Y: 308.05233015592455, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 147.02471465751842, Y: 318.2535850785045, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 129.96235453889085, Y: 322.1427838626073, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 123.08299511513388, Y: 340.9224114925356, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 116.2036356913769, Y: 359.7020391224639, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 119.26039879494844, Y: 376.93300541366887, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 110.46325463625759, Y: 392.06113334316535, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 110.46325463625759, Y: 412.06113334316535, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 110.46325463625759, Y: 432.06113334316535, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 127.9632546362576, Y: 432.06113334316535, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 145.4632546362576, Y: 432.06113334316535, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 162.9632546362576, Y: 432.06113334316535, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 180.4632546362576, Y: 432.06113334316535, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 197.9632546362576, Y: 432.06113334316535, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 215.4632546362576, Y: 432.06113334316535, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 232.9632546362576, Y: 432.06113334316535, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 232.9632546362576, Y: 412.06113334316535, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 232.9632546362576, Y: 392.0611333431654, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 224.11635454475476, Y: 376.96207673058063, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 227.08155965965068, Y: 359.71514336706156, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 240.4632667531364, Y: 348.4377736789105, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 257.9632425193788, Y: 348.4377736789105, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 271.3449496128645, Y: 359.71514336706156, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 274.31015472776045, Y: 376.96207673058063, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 265.4632546362576, Y: 392.0611333431654, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 265.4632546362576, Y: 412.0611333431654, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 265.4632546362576, Y: 432.0611333431654, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 282.9632546362576, Y: 432.0611333431654, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 300.4632546362576, Y: 432.0611333431654, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 317.9632546362576, Y: 432.0611333431654, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 335.4632546362576, Y: 432.0611333431654, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 352.9632546362576, Y: 432.0611333431654, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 8.713254636257588, Y: 452.06113334316535, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 63.832563384250136, Y: 340.02374123976233, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 30.24824292421914, Y: 217.93392629545838, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: -4.0, Y: 33.77371122170024, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 121.24772522748532, Y: 120.41819822359281, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 189.27280833088844, Y: 274.8961268421572, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 120.85539025998855, Y: 446.2032689668963, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 200.689021217243, Y: 380.5401422858765, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 296.7132546362576, Y: 452.0611333431654, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '83', X: 349.2132546362576, Y: 452.0611333431654, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'BCOR, -17.9 ± 1.2
 kcal/mol, AUC: 0.778', X: 114.4632546362576, Y: 464.8611333431654, Width: 142.5, Height: 23
Calculated bounding box: (-4.0, 5.0, 367.2132546362576, 464.8611333431654)
Updated viewBox: -9.0 0.0 381.2132546362576 469.8611333431654
Updated SVG: /disk1/www/rails/humanrnamap/public/result/de354a6a-2964-45d7-a8ac-59d6bc7b61cd/final_image/BCOR_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/de354a6a-2964-45d7-a8ac-59d6bc7b61cd/final_image/BCOR_fold_final_1.svg
