Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  5% [===                                               ] -                     
 10% [======                                            ] \                     
 15% [========                                          ] |                     
 20% [===========                                       ] /                     
 25% [=============                                     ] -                     
 30% [================                                  ] \                     
 36% [===================                               ] |                     
 41% [=====================                             ] /                     
 46% [========================                          ] -                     
 51% [==========================                        ] \                     
 56% [=============================                     ] |                     
 61% [===============================                   ] /                     
 67% [==================================                ] -                     
 72% [=====================================             ] \                     
 77% [=======================================           ] |                     
 82% [==========================================        ] /                     
 87% [============================================      ] -                     
 92% [===============================================   ] \                     
 97% [================================================= ] |                     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/68c9d200-e515-4abd-9a0a-977a85344dd2/final_image/HTT_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 156.64 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 156.64 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 156.64 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 170.16 MB
Based on canonical annotations, the following gene is in your area of interest: HTT(+)
write fasta - Elapsed time since the previous call: 0.64 seconds
write fasta - Current memory usage: 170.16 MB
Length of region: 97 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: 173.38 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/68c9d200-e515-4abd-9a0a-977a85344dd2/fasta/HTT.fasta" "/disk1/www/rails/humanrnamap/public/result/68c9d200-e515-4abd-9a0a-977a85344dd2/ct/HTT.ct" --SHAPE "HTT.dat"

fold - Elapsed time since the previous call: 0.11 seconds
fold - Current memory usage: 173.38 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/68c9d200-e515-4abd-9a0a-977a85344dd2/ct/HTT.ct" "/disk1/www/rails/humanrnamap/public/result/68c9d200-e515-4abd-9a0a-977a85344dd2/fold_FE/HTT.txt" -sh "HTT.dat"

efn2 - Elapsed time since the previous call: 0.51 seconds
efn2 - Current memory usage: 173.38 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/68c9d200-e515-4abd-9a0a-977a85344dd2/ct/HTT.ct" 1 "/disk1/www/rails/humanrnamap/public/result/68c9d200-e515-4abd-9a0a-977a85344dd2/fold_dbn/HTT_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 173.38 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AAAGCUACACACGCUAACUACAAGGUCACGCUGGAUCUUCAGAACAGCACGGAAAAGUUUGGAGGGUUUCUCCGCUCAGCCUUGGAUGUUCUUUCUC', '-structureDBN', '..(((.......)))......((((((......)))))).((((((.((.((...(((..((((.....)))))))...)).))..)))))).....', '-o', '/disk1/www/rails/humanrnamap/public/result/68c9d200-e515-4abd-9a0a-977a85344dd2/final_image/HTT_fold_1.svg', '-title', 'HTT, -20.7 ± 1.0\n kcal/mol, AUC: 0.753', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '4,6,13,15,19,24,25,26,30,32,33,34,36,38,39,42,47,51,52,57,58,59,60,61,62,64,65,66,67,68,69,71,74,76,79,82,83,84,85,87,88,89,90,92,93,94,96', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '72,81,35', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,3,70,9,10,73,16,80,18,27,31,37,41,45,46,48,53,54,63', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '2,5,7,8,11,12,75,14,77,78,17,20,21,22,23,86,91,28,29,95,97,40,43,44,49,50,55,56']
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 4.75, Y: 431.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 22.25, Y: 431.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 39.75, Y: 431.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 39.75, Y: 411.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 39.75, Y: 391.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 29.297923343555624, Y: 377.6130380794476, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 29.15087972320319, Y: 360.1136503586672, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 39.36561713592343, Y: 345.9041700016078, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 56.0, Y: 340.4684088626501, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 72.63438286407657, Y: 345.9041700016078, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 82.84912027679681, Y: 360.1136503586672, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 82.70207665644439, Y: 377.6130380794476, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 72.25, Y: 391.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 72.25, Y: 411.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 72.25, Y: 431.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 89.75, Y: 431.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 107.25, Y: 431.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 124.75, Y: 431.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 142.25, Y: 431.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 159.75, Y: 431.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 177.25, Y: 431.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 194.75, Y: 431.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 194.75, Y: 411.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 194.75, Y: 391.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 194.75, Y: 371.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 194.75, Y: 351.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 194.75, Y: 331.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 185.90309990849715, Y: 316.54980299594683, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 188.8683050233931, Y: 299.3028696324278, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 202.2500121168788, Y: 288.0254999442767, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 219.7499878831212, Y: 288.0254999442767, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 233.1316949766069, Y: 299.3028696324278, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 236.09690009150285, Y: 316.54980299594683, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 227.25, Y: 331.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 227.25, Y: 351.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 227.25, Y: 371.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 227.25, Y: 391.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 227.25, Y: 411.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 227.25, Y: 431.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 244.75, Y: 431.6488596085316, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 262.25, Y: 431.6488596085316, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 262.25, Y: 411.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 262.25, Y: 391.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 262.25, Y: 371.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 262.25, Y: 351.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 262.25, Y: 331.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 253.45286953776701, Y: 316.5208088866274, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 256.50954010935607, Y: 299.2899009584062, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 249.63006490963818, Y: 280.51031573997113, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 237.7952610025443, Y: 267.6190467240883, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 238.5021110971059, Y: 250.1334022320187, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 231.62257008054414, Y: 231.35384112422267, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 215.66674702692558, Y: 224.1662126216157, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 205.54687854813062, Y: 209.88900859625534, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 204.04928633153912, Y: 192.45319744900223, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 211.5863051501457, Y: 176.6594125910956, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 204.70677389716582, Y: 157.87984790659675, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 197.82724264418593, Y: 139.10028322209791, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 185.9923910456033, Y: 126.20902437958534, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 186.6992205900354, Y: 108.723354278035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 199.535973605325, Y: 96.82940460059035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 207.90884791745168, Y: 78.666393403288, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 216.28172222957832, Y: 60.503382205985645, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 224.65459654170496, Y: 42.34037100868329, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 225.39407893244376, Y: 24.855978722090867, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 238.26600871701754, Y: 13.0, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 255.75213455483356, Y: 13.69728833471504, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 267.6391402437256, Y: 26.540570765227585, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 266.9840500254473, Y: 44.028328329980695, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 254.16948973732121, Y: 55.9462917658891, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 245.79661542519455, Y: 74.10930296319145, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 237.42374111306793, Y: 92.2723141604938, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 229.0508668009413, Y: 110.43532535779616, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 228.34403525649643, Y: 127.92104493600573, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 235.2235665094763, Y: 146.70060962050445, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 242.10309776245617, Y: 165.48017430500317, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 258.0589103856274, Y: 172.66780559314327, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 268.1787721708572, Y: 186.945004108533, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 269.67636593775353, Y: 204.38080672583038, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 262.1393568807126, Y: 220.1745869723098, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 269.0188978972744, Y: 238.9541480801058, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 280.8537746254004, Y: 251.84545107204823, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 280.1468908895952, Y: 269.33116854042953, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 287.0263660893131, Y: 288.1107537588646, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 300.4903810551193, Y: 299.28976538783013, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 303.54714415869086, Y: 316.5207316790352, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 294.75, Y: 331.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 294.75, Y: 351.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 294.75, Y: 371.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 294.75, Y: 391.64885960853155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 294.75, Y: 411.6488596085316, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 294.75, Y: 431.6488596085316, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 312.25, Y: 431.6488596085316, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 329.75, Y: 431.6488596085316, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 347.25, Y: 431.6488596085316, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 364.75, Y: 431.6488596085316, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 382.25, Y: 431.6488596085316, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 5.5, Y: 451.64885960853155, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 80.69440410534716, Y: 329.763432773069, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 156.0, Y: 451.64885960853155, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 191.6395461804439, Y: 269.2389620212049, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 241.0, Y: 451.6488596085316, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 215.2656878393999, Y: 274.4985548322387, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 164.7862142834771, Y: 100.35046935658028, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 268.5925900883851, Y: 64.29724522224126, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 276.15474616671287, Y: 210.9881326227325, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '90', X: 311.0, Y: 391.64885960853155, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '97', X: 378.5, Y: 451.6488596085316, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'HTT, -20.7 ± 1.0
 kcal/mol, AUC: 0.753', X: 127.5, Y: 464.4488596085316, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 396.5, 464.4488596085316)
Updated viewBox: -0.25 0.0 401.75 469.4488596085316
Updated SVG: /disk1/www/rails/humanrnamap/public/result/68c9d200-e515-4abd-9a0a-977a85344dd2/final_image/HTT_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/68c9d200-e515-4abd-9a0a-977a85344dd2/final_image/HTT_fold_final_1.svg
