Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  4% [===                                               ] -                     
  9% [=====                                             ] \                     
 14% [========                                          ] |                     
 18% [==========                                        ] /                     
 23% [============                                      ] -                     
 28% [===============                                   ] \                     
 32% [=================                                 ] |                     
 37% [===================                               ] /                     
 42% [======================                            ] -                     
 46% [========================                          ] \                     
 51% [==========================                        ] |                     
 56% [=============================                     ] /                     
 60% [===============================                   ] -                     
 65% [=================================                 ] \                     
 70% [====================================              ] |                     
 74% [======================================            ] /                     
 79% [========================================          ] -                     
 84% [===========================================       ] \                     
 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/4177886f-1697-4b56-a6c5-d385ab441706/final_image/MALAT1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.84 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.84 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.84 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.48 MB
Based on canonical annotations, the following gene is in your area of interest: MALAT1(+)
write fasta - Elapsed time since the previous call: 0.56 seconds
write fasta - Current memory usage: 172.48 MB
Length of region: 107 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: 175.72 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/4177886f-1697-4b56-a6c5-d385ab441706/fasta/MALAT1.fasta" "/disk1/www/rails/humanrnamap/public/result/4177886f-1697-4b56-a6c5-d385ab441706/ct/MALAT1.ct" --SHAPE "MALAT1.dat"

fold - Elapsed time since the previous call: 0.14 seconds
fold - Current memory usage: 175.72 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/4177886f-1697-4b56-a6c5-d385ab441706/ct/MALAT1.ct" "/disk1/www/rails/humanrnamap/public/result/4177886f-1697-4b56-a6c5-d385ab441706/fold_FE/MALAT1.txt" -sh "MALAT1.dat"

efn2 - Elapsed time since the previous call: 0.42 seconds
efn2 - Current memory usage: 175.72 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/4177886f-1697-4b56-a6c5-d385ab441706/ct/MALAT1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/4177886f-1697-4b56-a6c5-d385ab441706/fold_dbn/MALAT1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.72 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CUGUGUGCCAAUGUUUCGUUUGCCUCAGACAGGUAUCUCUUCGUUAUCAGAAGAGUUGCUUCAUUUCAUCUGGGAGCAGAAAACAGCAGGCAGCUGUUAACAGAUAA', '-structureDBN', '((((.(((...(((((..(((((((((((.(((((.((((((.......)))))).))))).......)))))).))))))))))))).))))(((....)))....', '-o', '/disk1/www/rails/humanrnamap/public/result/4177886f-1697-4b56-a6c5-d385ab441706/final_image/MALAT1_fold_1.svg', '-title', 'MALAT1, -43.1 ± 1.6\n kcal/mol, AUC: 0.844', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,4,5,6,7,12,13,14,15,16,18,19,20,21,22,25,28,32,33,34,36,38,40,41,43,44,45,47,50,53,55,56,57,58,60,61,64,65,66,69,71,72,73,74,76,79,86,89,90,93,95,96,97,98,103,105', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '1,70,77,84,23,24,87,26,94,37,102,39,42,107,51,52,54,59', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '35,67,8,9,104,75,106,81,82,83,27,31', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '68,10,11,78,80,17,85,88,91,92,29,30,99,100,101,46,48,49,62,63']
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 22.779709535267813, Y: 517.9040389367276, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 22.779709535267813, Y: 497.9040389367276, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 22.779709535267813, Y: 477.9040389367276, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 22.779709535267813, Y: 457.9040389367276, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 16.101332383778555, Y: 441.7285025066448, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 22.779709535267813, Y: 425.5529660765621, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 22.779709535267813, Y: 405.5529660765621, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 22.779709535267784, Y: 385.5529660765621, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 13.982572224776135, Y: 370.424876750867, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 17.039289062281682, Y: 353.19393964108787, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 30.503232630273544, Y: 342.01489965083, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 48.00243229859953, Y: 342.17836975180563, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 65.3848743879903, Y: 332.28641812389236, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 82.76731647738103, Y: 322.39446649597903, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 100.1497585667718, Y: 312.5025148680657, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 117.53220065616253, Y: 302.61056324015243, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 128.2875960923944, Y: 288.80586346379306, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 145.64920733665892, Y: 286.60979381367696, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 159.50317216128303, Y: 297.3016563989897, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 178.80120254430307, Y: 302.5538962389091, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 198.09923292732307, Y: 307.8061360788285, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 217.39726331034308, Y: 313.0583759187479, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 236.69529369336308, Y: 318.3106157586673, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 254.17696794368317, Y: 319.1141112887661, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 273.87542604306043, Y: 315.65423433906454, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 293.5738841424378, Y: 312.194357389363, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 313.27234224181507, Y: 308.7344804396615, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 332.97080034119244, Y: 305.27460348996004, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 352.6692584405697, Y: 301.8147265402585, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 360.45824239305716, Y: 286.8004498066409, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 373.898701147598, Y: 276.53152360604696, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 373.898701147598, Y: 256.53152360604696, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 373.898701147598, Y: 236.53152360604696, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 373.898701147598, Y: 216.53152360604696, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 373.898701147598, Y: 196.53152360604696, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 367.22032399610873, Y: 180.35598717596412, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 373.898701147598, Y: 164.1804507458814, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 373.898701147598, Y: 144.1804507458814, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 373.898701147598, Y: 124.18045074588139, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 373.898701147598, Y: 104.18045074588139, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 373.898701147598, Y: 84.18045074588139, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 373.898701147598, Y: 64.18045074588139, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 363.44662449115356, Y: 50.144629216797455, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 363.29958087080115, Y: 32.64524149601698, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 373.51431828352133, Y: 18.43576113895756, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 390.148701147598, Y: 13.0, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 406.78308401167453, Y: 18.43576113895756, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 416.9978214243947, Y: 32.64524149601698, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 416.8507778040423, Y: 50.144629216797455, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 406.398701147598, Y: 64.18045074588139, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 406.398701147598, Y: 84.18045074588139, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 406.398701147598, Y: 104.18045074588139, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 406.398701147598, Y: 124.18045074588139, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 406.398701147598, Y: 144.1804507458814, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 406.398701147598, Y: 164.1804507458814, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 413.07707829908725, Y: 180.35598717596412, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 406.398701147598, Y: 196.53152360604696, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 406.398701147598, Y: 216.53152360604696, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 406.398701147598, Y: 236.53152360604696, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 406.398701147598, Y: 256.53152360604696, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 406.398701147598, Y: 276.53152360604696, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 420.3163138421173, Y: 287.3800194051818, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 427.9839662949057, Y: 303.27331705172907, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 427.81311640080526, Y: 320.91873046519663, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 419.8391599021387, Y: 336.66057984752365, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 405.71409729329787, Y: 347.2375553374649, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 388.36428143525166, Y: 350.4583772683365, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 371.38415184869325, Y: 345.65577344934627, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 358.2915584838347, Y: 333.82472095174666, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 338.59310038445744, Y: 337.2845979014482, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 318.89464228508007, Y: 340.7444748511497, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 299.1961841857028, Y: 344.20435180085116, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 279.49772608632543, Y: 347.6642287505527, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 259.79926798694817, Y: 351.12410570025423, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 243.63788868757882, Y: 357.8367668075884, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 228.160403953494, Y: 349.6699151310749, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 208.862373570474, Y: 344.4176752911555, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 189.564343187454, Y: 339.1654354512361, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 170.266312804434, Y: 333.91319561131667, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 150.968282421414, Y: 328.6609557713972, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 133.60662205152167, Y: 330.8570316354124, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 116.22417996213092, Y: 340.74898326332567, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 98.84173787274017, Y: 350.640934891239, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 81.4592957833494, Y: 360.5328865191523, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 64.07685369395864, Y: 370.4248381470656, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 55.279709535267784, Y: 385.5529660765621, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 55.279709535267784, Y: 405.5529660765621, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 55.27970953526781, Y: 425.5529660765621, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 61.95808668675707, Y: 441.7285025066448, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 55.27970953526781, Y: 457.9040389367276, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 55.27970953526781, Y: 477.9040389367276, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 55.27970953526781, Y: 497.9040389367276, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 55.27970953526781, Y: 517.9040389367276, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 72.77970953526781, Y: 517.9040389367276, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 72.77970953526781, Y: 497.9040389367276, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 72.77970953526781, Y: 477.9040389367276, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 69.2309751480287, Y: 460.76759426913645, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 80.27969165533483, Y: 447.1964073226026, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 97.7797274152008, Y: 447.1964073226026, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 108.8284439225069, Y: 460.7675942691364, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 105.27970953526781, Y: 477.9040389367276, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 105.27970953526781, Y: 497.9040389367276, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 105.27970953526781, Y: 517.9040389367276, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 122.77970953526781, Y: 517.9040389367276, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 140.2797095352678, Y: 517.9040389367276, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 157.7797095352678, Y: 517.9040389367276, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 175.2797095352678, Y: 517.9040389367276, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 23.529709535267813, Y: 537.9040389367276, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: -4.0, Y: 343.140060602584, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 180.30344238422248, Y: 283.25586585588906, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 341.3916249630561, Y: 273.9396088347999, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 350.148701147598, Y: 104.18045074588139, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 422.38644352968515, Y: 67.40868953171463, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 422.648701147598, Y: 256.53152360604696, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 338.302977334159, Y: 356.9830560008255, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 157.11026450946866, Y: 346.0433805265804, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '90', X: 71.52970953526781, Y: 457.9040389367276, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '100', X: 120.00734717523721, Y: 456.02231046349885, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '107', X: 167.0297095352678, Y: 537.9040389367276, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'MALAT1, -43.1 ± 1.6
 kcal/mol, AUC: 0.844', X: 154.98326925984094, Y: 550.7040389367276, Width: 142.5, Height: 23
Calculated bounding box: (-4.0, 5.0, 440.648701147598, 550.7040389367276)
Updated viewBox: -9.0 0.0 454.648701147598 555.7040389367276
Updated SVG: /disk1/www/rails/humanrnamap/public/result/4177886f-1697-4b56-a6c5-d385ab441706/final_image/MALAT1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/4177886f-1697-4b56-a6c5-d385ab441706/final_image/MALAT1_fold_final_1.svg
