Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  5% [===                                               ] -                     
 10% [======                                            ] \                     
 16% [=========                                         ] |                     
 21% [===========                                       ] /                     
 27% [==============                                    ] -                     
 32% [=================                                 ] \                     
 38% [====================                              ] |                     
 43% [======================                            ] /                     
 49% [=========================                         ] -                     
 54% [============================                      ] \                     
 60% [===============================                   ] |                     
 65% [=================================                 ] /                     
 71% [====================================              ] -                     
 76% [=======================================           ] \                     
 82% [==========================================        ] |                     
 87% [============================================      ] /                     
 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/3fce23fe-340c-4992-a6f2-b29424d30205/final_image/TFRC_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 157.00 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 157.00 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 157.00 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 170.57 MB
Based on canonical annotations, the following gene is in your area of interest: TFRC(-)
write fasta - Elapsed time since the previous call: 1.11 seconds
write fasta - Current memory usage: 170.57 MB
Length of region: 91 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: 173.86 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/3fce23fe-340c-4992-a6f2-b29424d30205/fasta/TFRC.fasta" "/disk1/www/rails/humanrnamap/public/result/3fce23fe-340c-4992-a6f2-b29424d30205/ct/TFRC.ct" --SHAPE "TFRC.dat"

fold - Elapsed time since the previous call: 0.10 seconds
fold - Current memory usage: 173.86 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/3fce23fe-340c-4992-a6f2-b29424d30205/ct/TFRC.ct" "/disk1/www/rails/humanrnamap/public/result/3fce23fe-340c-4992-a6f2-b29424d30205/fold_FE/TFRC.txt" -sh "TFRC.dat"

efn2 - Elapsed time since the previous call: 0.50 seconds
efn2 - Current memory usage: 173.86 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/3fce23fe-340c-4992-a6f2-b29424d30205/ct/TFRC.ct" 1 "/disk1/www/rails/humanrnamap/public/result/3fce23fe-340c-4992-a6f2-b29424d30205/fold_dbn/TFRC_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 173.86 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CUUUGGACAUGCUCAUCUGGGGACAGGUGACCCUUACACACCUGGAUUCCCUUCCUUCAAUCACACUCAGUUUCCACCAUCUCGGUCAUCA', '-structureDBN', '...((((...(((.....(((((((((((.........))))))...)))))................))).))))((.....))......', '-o', '/disk1/www/rails/humanrnamap/public/result/3fce23fe-340c-4992-a6f2-b29424d30205/final_image/TFRC_fold_1.svg', '-title', 'TFRC, -19.8 ± 0.9\n kcal/mol, AUC: 0.79', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,4,5,6,10,11,13,16,18,19,20,21,22,26,27,28,29,34,35,43,44,45,47,48,52,53,56,57,61,67,70,71,72,73,80,82,84,85,86,89', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '36,40,42,75,76,79,49,51,55,23,25', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '65,69,7,9,12,78,15,87,24,88,91,30,31,33,39,41,46,54,59,63', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,1,66,68,8,74,77,14,17,81,83,90,32,37,38,50,58,60,62']
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 153.5289656879488, Y: 351.58997435879735, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 171.0289656879488, Y: 351.58997435879735, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 188.5289656879488, Y: 351.58997435879735, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 206.0289656879488, Y: 351.58997435879735, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 206.0289656879488, Y: 331.58997435879735, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 206.0289656879488, Y: 311.58997435879735, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 206.0289656879488, Y: 291.58997435879735, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 195.64928179160898, Y: 277.5005333757308, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 195.6492835284235, Y: 260.0005280899245, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 206.02897022141883, Y: 245.91108916715308, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 222.74256028102332, Y: 240.72398088577495, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 234.60505737380024, Y: 224.6217710149573, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 246.46755446657716, Y: 208.51956114413957, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 237.35338260522428, Y: 195.46590810013333, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 231.21515339522284, Y: 180.7761794206424, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 228.33216294382487, Y: 165.1187737425385, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 228.8355904531703, Y: 149.20612005893167, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 232.70252942387094, Y: 133.76226142488395, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 239.75702992565402, Y: 119.48991021066865, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 225.61489430192307, Y: 105.3477745869377, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 211.47275867819212, Y: 91.20563896320675, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 197.33062305446117, Y: 77.0635033394758, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 183.18848743073022, Y: 62.92136771574485, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 166.27089385331874, Y: 58.444775977935706, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 146.98501775673432, Y: 63.74147147486519, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 127.6991416601499, Y: 69.0381669717948, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 108.41326556356549, Y: 74.33486246872428, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 89.12738946698107, Y: 79.63155796565388, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 69.84151337039668, Y: 84.92825346258337, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 61.439429075361545, Y: 100.27929432603469, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 46.454098593050844, Y: 109.31751021348487, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 28.956199819081235, Y: 109.58772233042646, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 13.698935216556208, Y: 101.01652912639918, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 4.8268520037295275, Y: 85.93224539939024, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 4.75, Y: 68.43242911859033, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 13.489255605336723, Y: 53.27080362668414, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 28.670650847609636, Y: 44.565936333604895, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 46.170247979146666, Y: 44.682453826403275, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 61.234383187886124, Y: 53.58870480563371, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 80.52025928447057, Y: 48.29200930870422, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 99.80613538105496, Y: 42.99531381177462, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 119.0920114776394, Y: 37.698618314845135, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 138.3778875742238, Y: 32.40192281791553, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 157.6637636708082, Y: 27.105227320986046, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 169.92193401932667, Y: 14.615741354513943, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 187.3471852334502, Y: 13.0, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 201.69277626337436, Y: 23.022675191891608, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 206.169457819293, Y: 39.94039732718204, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 220.31159344302395, Y: 54.08253295091299, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 234.4537290667549, Y: 68.22466857464394, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 248.59586469048588, Y: 82.3668041983749, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 262.73800031421683, Y: 96.50893982210584, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 279.03909631459277, Y: 88.74182574482563, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 296.7284510901304, Y: 85.11684029270054, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 314.77067613247596, Y: 85.84616012947583, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 332.1097288266771, Y: 90.88709690458745, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 347.7307244506441, Y: 99.9445958761005, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 360.71933913200667, Y: 112.48850597471193, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 370.3153268046327, Y: 127.78461046212192, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 375.9570177248478, Y: 144.93760190570748, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 377.3141939722925, Y: 162.94348606995584, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 374.3074176755328, Y: 180.74834743431916, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 367.11268064797036, Y: 197.31003669016428, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 356.1511032828299, Y: 211.65916954100226, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 342.06428564870157, Y: 222.95586644079413, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 325.6767535286185, Y: 230.53891219538377, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 307.94769750090956, Y: 233.96445803062153, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 289.9148298568358, Y: 233.0320008282393, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 272.6336455066559, Y: 227.79611891990209, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 260.771148413879, Y: 243.8983287907198, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 248.90865132110207, Y: 260.00053866153746, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 248.90864784747419, Y: 277.5005386615371, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 238.5289656879488, Y: 291.58997435879735, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 238.5289656879488, Y: 311.58997435879735, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 238.5289656879488, Y: 331.58997435879735, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 238.5289656879488, Y: 351.58997435879735, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 256.0289656879488, Y: 351.58997435879735, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 256.0289656879488, Y: 331.58997435879735, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 249.38079608313092, Y: 315.4019340591428, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 256.10701533917035, Y: 299.24616783288934, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 272.2789656879488, Y: 292.5589539321449, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 288.45091603672734, Y: 299.24616783288934, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 295.1771352927667, Y: 315.4019340591428, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 288.5289656879488, Y: 331.58997435879735, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 288.5289656879488, Y: 351.58997435879735, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 306.0289656879488, Y: 351.58997435879735, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 323.5289656879488, Y: 351.58997435879735, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 341.0289656879488, Y: 351.58997435879735, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 358.5289656879488, Y: 351.58997435879735, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 376.0289656879488, Y: 351.58997435879735, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 393.5289656879488, Y: 351.5899743587974, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 154.2789656879488, Y: 371.58997435879735, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 190.6844133666783, Y: 229.61488558036055, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 207.72275867819212, Y: 119.48991021066865, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 72.12494160057925, Y: 114.1218366551837, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 71.47356378754098, Y: 29.006133212119835, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 244.84586469048583, Y: 54.08253295091299, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 391.8221539371304, Y: 141.03293401027764, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 273.12335828469674, Y: 255.76082588349675, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 238.23195334334048, Y: 285.0869791691995, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '90', X: 372.2789656879488, Y: 371.58997435879735, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '91', X: 389.7789656879488, Y: 371.5899743587974, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'TFRC, -19.8 ± 0.9
 kcal/mol, AUC: 0.79', X: 137.6394828439744, Y: 384.3899743587974, Width: 133.5, Height: 23
Calculated bounding box: (4.75, 5.0, 409.8221539371304, 384.3899743587974)
Updated viewBox: -0.25 0.0 415.0721539371304 389.3899743587974
Updated SVG: /disk1/www/rails/humanrnamap/public/result/3fce23fe-340c-4992-a6f2-b29424d30205/final_image/TFRC_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/3fce23fe-340c-4992-a6f2-b29424d30205/final_image/TFRC_fold_final_1.svg
