Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  5% [===                                               ] -                     
 10% [======                                            ] \                     
 15% [========                                          ] |                     
 20% [===========                                       ] /                     
 25% [=============                                     ] -                     
 30% [================                                  ] \                     
 35% [==================                                ] |                     
 40% [=====================                             ] /                     
 45% [=======================                           ] -                     
 51% [==========================                        ] \                     
 56% [=============================                     ] |                     
 61% [===============================                   ] /                     
 66% [==================================                ] -                     
 71% [====================================              ] \                     
 76% [=======================================           ] |                     
 81% [=========================================         ] /                     
 86% [============================================      ] -                     
 91% [==============================================    ] \                     
 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/9bd33815-616a-4e0b-a13b-7ad2d3222315/final_image/MLLT6_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.93 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.93 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.93 MB
read annotations - Elapsed time since the previous call: 0.10 seconds
read annotations - Current memory usage: 172.64 MB
Based on canonical annotations, the following gene is in your area of interest: MLLT6(+)
write fasta - Elapsed time since the previous call: 0.66 seconds
write fasta - Current memory usage: 172.64 MB
Length of region: 98 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: 176.20 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/9bd33815-616a-4e0b-a13b-7ad2d3222315/fasta/MLLT6.fasta" "/disk1/www/rails/humanrnamap/public/result/9bd33815-616a-4e0b-a13b-7ad2d3222315/ct/MLLT6.ct" --SHAPE "MLLT6.dat"

fold - Elapsed time since the previous call: 0.15 seconds
fold - Current memory usage: 176.20 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/9bd33815-616a-4e0b-a13b-7ad2d3222315/ct/MLLT6.ct" "/disk1/www/rails/humanrnamap/public/result/9bd33815-616a-4e0b-a13b-7ad2d3222315/fold_FE/MLLT6.txt" -sh "MLLT6.dat"

efn2 - Elapsed time since the previous call: 0.43 seconds
efn2 - Current memory usage: 176.20 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/9bd33815-616a-4e0b-a13b-7ad2d3222315/ct/MLLT6.ct" 1 "/disk1/www/rails/humanrnamap/public/result/9bd33815-616a-4e0b-a13b-7ad2d3222315/fold_dbn/MLLT6_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 176.20 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AGCCCCAGGGCUUGGGGGAGGGCGUAAGGUGGGGGGAAAUGCCACUGCUUUUAGCAAAAGCCUCCCUCCCAGAAUUAGCCAGCUUGCCUCCUGCACCC', '-structureDBN', '((((....)))).(.((((((.((...((((((((((...((...((((...))))...)).)))))))........)))....)))))))).)....', '-o', '/disk1/www/rails/humanrnamap/public/result/9bd33815-616a-4e0b-a13b-7ad2d3222315/final_image/MLLT6_fold_1.svg', '-title', 'MLLT6, -40.9 ± 1.5\n kcal/mol, AUC: 0.595', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,8,9,10,12,13,14,15,16,17,18,20,21,22,24,25,28,29,30,31,32,33,34,35,36,40,41,46,47,49,50,51,52,54,60,63,67,72,75,76,78,82,84,85,86,89,92,93', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '65,66,68,5,69,77,80,81,83,88,91,96,97,42,43,61,62', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '64,1,4,70,7,71,79,19,90,95,98,37,44,48,53,59', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '3,6,73,74,11,87,23,26,27,94,38,39,45,55,56,57,58']
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 217.16432769692, Y: 440.159318870206, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 217.16432769692, Y: 420.159318870206, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 217.16432769692, Y: 400.159318870206, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 217.16432769692, Y: 380.159318870206, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 213.6155933096809, Y: 363.02287420261484, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 224.66430981698701, Y: 349.4516872560811, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 242.16434557685298, Y: 349.4516872560811, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 253.21306208415905, Y: 363.02287420261484, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 249.66432769692003, Y: 380.159318870206, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 249.66432769692003, Y: 400.159318870206, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 249.66432769692003, Y: 420.159318870206, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 249.66432769692003, Y: 440.159318870206, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 267.16432769692, Y: 440.159318870206, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 284.66432769692, Y: 440.159318870206, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 277.98595054543074, Y: 423.98378244012326, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 284.66432769691994, Y: 407.8082460100405, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 284.66432769692, Y: 387.8082460100404, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 284.66432769692, Y: 367.80824601004053, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 284.66432769692, Y: 347.80824601004053, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 284.66432769692, Y: 327.80824601004053, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 284.66432769692, Y: 307.80824601004053, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 280.84870883033733, Y: 290.7292143486055, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 291.57004978947674, Y: 276.8979050156031, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 300.0816678047246, Y: 258.7994973850266, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 292.9707556143537, Y: 242.80926394359838, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 294.227438121703, Y: 225.35436816143292, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 303.5556050011504, Y: 210.54768249718938, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 318.75727345594646, Y: 201.87808539692026, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 322.62186738069965, Y: 182.25501443958126, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 326.48646130545285, Y: 162.63194348224238, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 314.03270561876815, Y: 147.48631092824792, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 294.03270561876815, Y: 147.48631092824792, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 274.03270561876815, Y: 147.48631092824792, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 254.03270561876815, Y: 147.48631092824792, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 234.03270561876818, Y: 147.48631092824792, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 214.03270561876818, Y: 147.48631092824792, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 194.03270561876818, Y: 147.48631092824792, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 179.94326463570164, Y: 157.8659948245877, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 162.44325934989533, Y: 157.86599308777318, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 148.3538204271239, Y: 147.4863063947779, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 143.16671214574578, Y: 130.7727163351734, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 127.06450227492806, Y: 118.91021924239647, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 109.79212643407512, Y: 121.72363809180229, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 93.4730221309783, Y: 115.40405522941967, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 82.60035786220551, Y: 101.69145283204716, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 80.16772394122388, Y: 84.36134651337852, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 64.06552023777563, Y: 72.49884104898945, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 47.963316534327376, Y: 60.63633558460049, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 31.861112830879122, Y: 48.77383012021153, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 18.34967238098655, Y: 37.65214999257728, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 20.605319208721614, Y: 20.298105816047723, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 36.5109296462427, Y: 13.0, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 51.13768421051118, Y: 22.607749102108187, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 67.23988791395944, Y: 34.47025456649715, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 83.34209161740769, Y: 46.33276003088611, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 99.44429532085594, Y: 58.195265495275066, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 116.71666400156603, Y: 55.38185472583086, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 133.03575968181266, Y: 61.701436688188664, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 143.90842053514697, Y: 75.41403111697457, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 146.34106005069057, Y: 92.74412820231771, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 162.44326992150826, Y: 104.60662529509466, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 179.94326992150792, Y: 104.60662876872254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 194.03270561876818, Y: 114.98631092824792, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 214.03270561876818, Y: 114.98631092824792, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 234.03270561876818, Y: 114.98631092824792, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 254.03270561876815, Y: 114.98631092824792, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 274.03270561876815, Y: 114.98631092824792, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 294.03270561876815, Y: 114.98631092824792, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 314.03270561876815, Y: 114.98631092824792, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 324.57786704445147, Y: 101.31608099262849, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 340.0122843412834, Y: 93.57951982543807, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 357.2750612504393, Y: 93.3109134756669, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 372.9427080319465, Y: 100.56353095602185, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 383.9080752226409, Y: 113.89906013036159, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 387.99655196646347, Y: 130.67284842942047, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 384.39732675503114, Y: 147.55838051650073, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 373.8241845516805, Y: 161.20698044228607, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 358.3739516111287, Y: 168.9119086099663, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 354.5093576863755, Y: 188.5349795673052, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 350.6447637616223, Y: 208.15805052464418, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 361.42390632131463, Y: 221.94427864105919, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 364.44119113898756, Y: 239.18220172735468, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 358.9856657747545, Y: 255.8101072779708, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 346.3427968991289, Y: 267.9100191203661, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 329.4915802044114, Y: 272.63087665980436, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 320.97996218916353, Y: 290.72928429038086, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 317.16432769692, Y: 307.80824601004053, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 317.16432769692, Y: 327.80824601004053, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 317.16432769692, Y: 347.80824601004053, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 317.16432769692, Y: 367.80824601004053, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 317.16432769692, Y: 387.8082460100404, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 317.16432769692, Y: 407.8082460100404, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 323.84270484840926, Y: 423.98378244012326, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 317.16432769692, Y: 440.159318870206, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 334.66432769692, Y: 440.159318870206, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 352.16432769692, Y: 440.159318870206, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 369.66432769692, Y: 440.159318870206, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 387.16432769692, Y: 440.159318870206, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 217.91432769692, Y: 460.159318870206, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 265.91432769692, Y: 400.159318870206, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 260.91432769692, Y: 327.80824601004053, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 303.11339034811385, Y: 158.76734955748918, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 128.30761684033138, Y: 159.08086324951842, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: -4.0, Y: 45.00416926077605, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 150.82291959972278, Y: 74.5167727066621, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 308.1095294033391, Y: 85.88092995201134, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 366.7694720998671, Y: 205.92288420651425, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '90', X: 333.41432769692, Y: 367.80824601004053, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '98', X: 383.41432769692, Y: 460.159318870206, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'MLLT6, -40.9 ± 1.5
 kcal/mol, AUC: 0.595', X: 137.17311217372503, Y: 472.959318870206, Width: 142.5, Height: 23
Calculated bounding box: (-4.0, 5.0, 401.41432769692, 472.959318870206)
Updated viewBox: -9.0 0.0 415.41432769692 477.959318870206
Updated SVG: /disk1/www/rails/humanrnamap/public/result/9bd33815-616a-4e0b-a13b-7ad2d3222315/final_image/MLLT6_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/9bd33815-616a-4e0b-a13b-7ad2d3222315/final_image/MLLT6_fold_final_1.svg
