Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  5% [===                                               ] -                     
 10% [======                                            ] \                     
 15% [========                                          ] |                     
 20% [===========                                       ] /                     
 26% [==============                                    ] -                     
 31% [================                                  ] \                     
 36% [===================                               ] |                     
 41% [=====================                             ] /                     
 46% [========================                          ] -                     
 52% [===========================                       ] \                     
 57% [=============================                     ] |                     
 62% [================================                  ] /                     
 67% [==================================                ] -                     
 72% [=====================================             ] \                     
 78% [========================================          ] |                     
 83% [==========================================        ] /                     
 88% [=============================================     ] -                     
 93% [===============================================   ] \                     
 98% [==================================================] |                     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/50fb8837-3da2-45e7-aa58-da2c781eccc0/final_image/TNRC18_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.43 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.43 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.43 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.03 MB
Based on canonical annotations, the following gene is in your area of interest: TNRC18(-)
write fasta - Elapsed time since the previous call: 0.48 seconds
write fasta - Current memory usage: 172.03 MB
Length of region: 96 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: 0.20 seconds
write dat - Current memory usage: 175.65 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/50fb8837-3da2-45e7-aa58-da2c781eccc0/fasta/TNRC18.fasta" "/disk1/www/rails/humanrnamap/public/result/50fb8837-3da2-45e7-aa58-da2c781eccc0/ct/TNRC18.ct" --SHAPE "TNRC18.dat"

fold - Elapsed time since the previous call: 0.12 seconds
fold - Current memory usage: 175.65 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/50fb8837-3da2-45e7-aa58-da2c781eccc0/ct/TNRC18.ct" "/disk1/www/rails/humanrnamap/public/result/50fb8837-3da2-45e7-aa58-da2c781eccc0/fold_FE/TNRC18.txt" -sh "TNRC18.dat"

efn2 - Elapsed time since the previous call: 0.51 seconds
efn2 - Current memory usage: 175.65 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/50fb8837-3da2-45e7-aa58-da2c781eccc0/ct/TNRC18.ct" 1 "/disk1/www/rails/humanrnamap/public/result/50fb8837-3da2-45e7-aa58-da2c781eccc0/fold_dbn/TNRC18_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.65 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CUGAAACCCAAGCCGGCCACCAGCAGGAAGCAGCCGUUUUGUCUGCUGCUUCGAGAGGCCGAGGCGCGUUCCUCCUUCAGCGACUCUUCGGAGGAA', '-structureDBN', '...........(((((((........((((((((..........))))))))....)))))....)).(((((((..............)))))))', '-o', '/disk1/www/rails/humanrnamap/public/result/50fb8837-3da2-45e7-aa58-da2c781eccc0/final_image/TNRC18_fold_1.svg', '-title', 'TNRC18, -38.1 ± 1.6\n kcal/mol, AUC: 0.927', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,12,15,16,23,26,27,30,33,36,37,38,39,40,41,42,44,45,47,48,50,51,53,55,57,58,61,63,64,66,68,69,70,73,76,77,80,82,85,87,88,90,91,93,94', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '34,71,72,74,75,46,60,49,18,52,28,29', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '32,65,96,35,43,13,14,17,19,20,21,86,59,95,31', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,67,4,5,6,7,8,9,10,11,78,79,81,83,84,22,24,25,89,92,54,56,62']
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 91.66651690315007, Y: 334.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 109.16651690315007, Y: 334.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 126.66651690315007, Y: 334.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 144.16651690315007, Y: 334.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 161.66651690315007, Y: 334.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 179.16651690315007, Y: 334.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 196.66651690315007, Y: 334.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 214.16651690315007, Y: 334.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 231.66651690315007, Y: 334.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 249.16651690315007, Y: 334.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 266.66651690315007, Y: 334.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 284.16651690315007, Y: 334.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 284.16651690315007, Y: 314.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 273.78682779637313, Y: 300.28863534271284, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 254.68559307853906, Y: 294.36049632155175, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 235.58435836070504, Y: 288.4323573003907, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 216.48312364287102, Y: 282.5042182792297, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 197.381888925037, Y: 276.5760792580686, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 184.69940200843726, Y: 288.63445010871305, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 168.62530755270762, Y: 295.5535013001465, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 151.1496774024674, Y: 296.47661170167487, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 134.4361021490719, Y: 291.2894945629859, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 120.55382529649049, Y: 280.6343469173793, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 111.22155817739699, Y: 265.8303416357238, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 107.59469290991817, Y: 248.71030570430855, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 110.12225774089649, Y: 231.39380496118508, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 118.49132458474475, Y: 216.02472879751815, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 107.82586996097481, Y: 199.10586129202875, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 97.16041533720488, Y: 182.18699378653935, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 86.49496071343492, Y: 165.26812628105, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 75.82950608966499, Y: 148.34925877556066, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 65.16405146589506, Y: 131.43039127007125, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 54.498596842125096, Y: 114.51152376458185, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 43.833142218355164, Y: 97.59265625909251, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 26.516872889578167, Y: 95.06363881317179, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 12.395450322084969, Y: 84.72755941241212, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 4.75, Y: 68.98601558465981, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 5.356949317199678, Y: 51.49656947465206, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 14.07527304320763, Y: 36.32290992538566, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 28.879260664828053, Y: 26.990650648692565, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 46.32919208163881, Y: 25.66815064600229, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 62.37055972584571, Y: 32.66269400578693, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 73.276137113994, Y: 46.3490921637985, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 76.51200333858861, Y: 63.54729795641077, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 71.3263019147754, Y: 80.26129249546636, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 81.99175653854536, Y: 97.18016000095577, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 92.65721116231529, Y: 114.09902750644511, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 103.32266578608522, Y: 131.01789501193446, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 113.98812040985518, Y: 147.93676251742386, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 124.65357503362512, Y: 164.85563002291326, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 135.31902965739505, Y: 181.7744975284026, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 145.984484281165, Y: 198.69336503389195, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 163.46012041749276, Y: 197.77024985653043, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 180.1737022806256, Y: 202.95736671509042, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 194.05598407504198, Y: 213.61251815373345, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 203.3882526325786, Y: 228.4165298927863, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 207.01511483442374, Y: 245.53657284158834, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 226.11634955225776, Y: 251.4647118627494, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 245.21758427009178, Y: 257.39285088391046, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 264.3188189879258, Y: 263.3209899050715, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 283.4200537057598, Y: 269.2491289262326, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 299.9529445623763, Y: 263.51209834210556, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 316.6665259700882, Y: 268.6992166680923, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 327.0462025363033, Y: 282.7886564859404, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 327.04619906267544, Y: 300.28865648594007, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 316.66651690315007, Y: 314.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 316.66651690315007, Y: 334.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 334.16651690315007, Y: 334.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 351.66651690315007, Y: 334.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 351.66651690315007, Y: 314.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 351.66651690315007, Y: 294.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 351.66651690315007, Y: 274.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 351.66651690315007, Y: 254.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 351.66651690315007, Y: 234.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 351.66651690315007, Y: 214.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 336.6274916792741, Y: 205.4294846207, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 325.87138997380663, Y: 191.6252775412022, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 320.870535089603, Y: 174.85502687464532, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 322.30945710845555, Y: 157.41428834625503, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 329.99119262509345, Y: 141.69039581150275, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 342.86424561268313, Y: 129.83567676081555, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 359.1665189461215, Y: 123.47283610951229, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 376.6665148601786, Y: 123.47283610951229, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 392.96878819361706, Y: 129.8356767608156, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 405.8418411812067, Y: 141.69039581150275, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 413.52357669784465, Y: 157.4142883462551, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 414.96249871669716, Y: 174.85502687464532, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 409.9616438324935, Y: 191.6252775412022, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 399.20554212702604, Y: 205.4294846207, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 384.16651690315007, Y: 214.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 384.16651690315007, Y: 234.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 384.16651690315007, Y: 254.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 384.16651690315007, Y: 274.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 384.16651690315007, Y: 294.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 384.16651690315007, Y: 314.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 384.16651690315007, Y: 334.37809218320035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 92.41651690315007, Y: 354.37809218320035, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 245.41651690315007, Y: 354.37809218320035, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 169.42754749247658, Y: 315.02853946521236, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 65.82609320794555, Y: 175.93358090481996, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 18.855889327236724, Y: 8.0, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 137.82244253911452, Y: 154.19017539914336, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 266.4969580090869, Y: 244.21975518723747, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 327.91651690315007, Y: 314.37809218320035, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 310.2052130606209, Y: 129.7385189962147, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '90', X: 398.64560098961516, Y: 222.6061231365078, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '96', X: 380.41651690315007, Y: 354.37809218320035, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'TNRC18, -38.1 ± 1.6
 kcal/mol, AUC: 0.927', X: 143.85624935834858, Y: 367.17809218320036, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 425.46249871669716, 367.17809218320036)
Updated viewBox: -0.25 -5.0 430.71249871669716 377.17809218320036
Updated SVG: /disk1/www/rails/humanrnamap/public/result/50fb8837-3da2-45e7-aa58-da2c781eccc0/final_image/TNRC18_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/50fb8837-3da2-45e7-aa58-da2c781eccc0/final_image/TNRC18_fold_final_1.svg
