Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  6% [====                                              ] -                     
 12% [=======                                           ] \                     
 18% [==========                                        ] |                     
 25% [=============                                     ] /                     
 31% [================                                  ] -                     
 37% [===================                               ] \                     
 43% [======================                            ] |                     
 50% [==========================                        ] /                     
 56% [=============================                     ] -                     
 62% [================================                  ] \                     
 68% [===================================               ] |                     
 75% [======================================            ] /                     
 81% [=========================================         ] -                     
 87% [============================================      ] \                     
 93% [===============================================   ] |                     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/7b70d258-c7ec-493c-9262-d2dfaf7949f0/final_image/ADAR_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.50 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.50 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.50 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.05 MB
Based on canonical annotations, the following gene is in your area of interest: ADAR(-)
write fasta - Elapsed time since the previous call: 2.00 seconds
write fasta - Current memory usage: 172.05 MB
Length of region: 80 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: 175.68 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/7b70d258-c7ec-493c-9262-d2dfaf7949f0/fasta/ADAR.fasta" "/disk1/www/rails/humanrnamap/public/result/7b70d258-c7ec-493c-9262-d2dfaf7949f0/ct/ADAR.ct" --SHAPE "ADAR.dat"

fold - Elapsed time since the previous call: 0.09 seconds
fold - Current memory usage: 175.68 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/7b70d258-c7ec-493c-9262-d2dfaf7949f0/ct/ADAR.ct" "/disk1/www/rails/humanrnamap/public/result/7b70d258-c7ec-493c-9262-d2dfaf7949f0/fold_FE/ADAR.txt" -sh "ADAR.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 175.68 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/7b70d258-c7ec-493c-9262-d2dfaf7949f0/ct/ADAR.ct" 1 "/disk1/www/rails/humanrnamap/public/result/7b70d258-c7ec-493c-9262-d2dfaf7949f0/fold_dbn/ADAR_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.68 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AGAAAGAAUCAGAGAAGACUGCAGAGUCCCAGACCCCCACCCCUUCAGCCACAUCCUUCUUUUCUGGGAAGAGCCCCGUC', '-structureDBN', '................(((.((....(((((((.............................)))))))...))...)))', '-o', '/disk1/www/rails/humanrnamap/public/result/7b70d258-c7ec-493c-9262-d2dfaf7949f0/final_image/ADAR_fold_1.svg', '-title', 'ADAR, -13.7 ± 0.6\n kcal/mol, AUC: 0.713', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '65,2,66,67,68,6,71,9,73,12,14,78,79,17,20,21,24,26,27,32,44,45,48,54,57,58,60,61,62,63', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '35,36,40,41,74,75,76,56,28,29', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '64,7,11,77,16,80,18,19,22,23,30,31,33,39,42,50,53,55', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,3,4,5,69,70,8,72,10,13,15,25,34,37,38,43,46,47,49,51,52,59']
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 4.75, Y: 461.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 22.25, Y: 461.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 39.75, Y: 461.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 57.25, Y: 461.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 74.75, Y: 461.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 92.25, Y: 461.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 109.75, Y: 461.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 127.25, Y: 461.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 144.75, Y: 461.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 162.25, Y: 461.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 179.75, Y: 461.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 197.25, Y: 461.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 214.75, Y: 461.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 232.25, Y: 461.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 249.75, Y: 461.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 267.25, Y: 461.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 284.75, Y: 461.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 284.75, Y: 441.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 284.75, Y: 421.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 274.37031436684674, Y: 407.650937748478, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 274.3703213141068, Y: 390.15092717686673, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 262.5078370060388, Y: 374.0487078875625, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 245.06073700595533, Y: 372.68826246834806, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 230.30978673949528, Y: 363.27223483521107, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 221.73072581240712, Y: 348.01930646847165, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 221.34502276100665, Y: 330.5234971614485, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 229.24356009439293, Y: 314.90731266763953, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 221.64396751189543, Y: 296.4074155711677, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 214.04437492939792, Y: 277.90751847469585, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 206.4447823469004, Y: 259.407621378224, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 198.8451897644029, Y: 240.90772428175205, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 191.2455971819054, Y: 222.40782718528027, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 183.6460045994079, Y: 203.9079300888083, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 166.24672159255536, Y: 205.78288250824681, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 148.81727955157902, Y: 204.21283605417221, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 132.03316725033216, Y: 199.25863884505355, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 116.54486331067372, Y: 191.11229384864765, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 102.95262650237217, Y: 180.08951768858907, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 91.7832323443441, Y: 166.61750485195938, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 83.46955759459206, Y: 151.21837150351934, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 78.33380384452222, Y: 134.48892055178902, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 76.57501039758974, Y: 117.07751218432094, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 78.26134037835911, Y: 99.65893626883172, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 83.32743902858029, Y: 82.90826045578063, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 91.57696657114435, Y: 67.4746675153088, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 102.69020747921486, Y: 53.95629585867454, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 116.23646124861742, Y: 42.87705831529405, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 131.69073446146245, Y: 34.66633756797552, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 148.45408722978362, Y: 29.642345162276285, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 165.87684548022156, Y: 27.9997890218346, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 183.28377947334675, Y: 29.802327422726478, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 200.00027274857945, Y: 34.98010187772189, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 215.37846730111022, Y: 43.33244454503523, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 228.8223717183654, Y: 54.53565523427113, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 239.81095919471022, Y: 68.15554660690799, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 247.91836024658164, Y: 83.66427137433533, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 252.83036754693023, Y: 100.46077934501278, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 254.3566132239289, Y: 117.89411149526876, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 252.43794668523333, Y: 135.28862828766609, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 247.1487270356622, Y: 151.97019449789644, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 238.69394124423792, Y: 167.29230574109118, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 227.40125974780028, Y: 180.66114414791315, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 213.70833738117472, Y: 191.5585921422499, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 221.30792996367222, Y: 210.05848923872173, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 228.90752254616973, Y: 228.5583863351937, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 236.50711512866724, Y: 247.0582834316655, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 244.10670771116474, Y: 265.5581805281373, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 251.70630029366225, Y: 284.05807762460927, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 259.30589287615976, Y: 302.5579747210811, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 275.90105292866195, Y: 308.1123120201506, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 287.92554661039463, Y: 320.82693162507667, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 292.5460838483241, Y: 337.7059314660894, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 288.6739433511583, Y: 354.77217088695215, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 300.5364276592262, Y: 370.8743901762564, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 317.2500090669381, Y: 376.0615085022431, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 327.62968563315326, Y: 390.1509483200913, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 327.6296821595253, Y: 407.65094832009095, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 317.25, Y: 421.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 317.25, Y: 441.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 317.25, Y: 461.7403840173512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 5.5, Y: 481.7403840173512, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 158.5, Y: 481.7403840173512, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 251.6197303523212, Y: 413.8941586405302, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 184.1948852504285, Y: 267.00721396072146, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 61.27078971343488, Y: 158.94125721206012, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 162.21870995705544, Y: 8.0, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 261.7757713263604, Y: 159.8622311892529, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 282.912219354066, Y: 291.25415977369266, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 313.5, Y: 481.7403840173512, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'ADAR, -13.7 ± 0.6
 kcal/mol, AUC: 0.713', X: 100.18984281657663, Y: 494.5403840173512, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 338.12968563315326, 494.5403840173512)
Updated viewBox: -0.25 -5.0 343.37968563315326 504.5403840173512
Updated SVG: /disk1/www/rails/humanrnamap/public/result/7b70d258-c7ec-493c-9262-d2dfaf7949f0/final_image/ADAR_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/7b70d258-c7ec-493c-9262-d2dfaf7949f0/final_image/ADAR_fold_final_1.svg
