Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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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/b9ea3d8d-07a1-4469-bb29-7b404a74680c/final_image/MIR3648_1_1_181_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.00 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.00 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.00 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 171.62 MB
Based on canonical annotations, the following gene is in your area of interest: MIR3648-1(+)
write fasta - Elapsed time since the previous call: 0.13 seconds
write fasta - Current memory usage: 171.62 MB
Length of region: 180 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: 0.23 seconds
write dat - Current memory usage: 175.15 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/b9ea3d8d-07a1-4469-bb29-7b404a74680c/fasta/MIR3648_1_1_181.fasta" "/disk1/www/rails/humanrnamap/public/result/b9ea3d8d-07a1-4469-bb29-7b404a74680c/ct/MIR3648_1_1_181.ct" --SHAPE "MIR3648_1_1_181.dat"

fold - Elapsed time since the previous call: 0.53 seconds
fold - Current memory usage: 175.15 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/b9ea3d8d-07a1-4469-bb29-7b404a74680c/ct/MIR3648_1_1_181.ct" "/disk1/www/rails/humanrnamap/public/result/b9ea3d8d-07a1-4469-bb29-7b404a74680c/fold_FE/MIR3648_1_1_181.txt" -sh "MIR3648_1_1_181.dat"

efn2 - Elapsed time since the previous call: 0.52 seconds
efn2 - Current memory usage: 175.15 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/b9ea3d8d-07a1-4469-bb29-7b404a74680c/ct/MIR3648_1_1_181.ct" 1 "/disk1/www/rails/humanrnamap/public/result/b9ea3d8d-07a1-4469-bb29-7b404a74680c/fold_dbn/MIR3648_1_1_181_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.15 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CGCGACUGCGGCGGCGGUGGUGGGGGGAGCCGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUGCCGCCGGCGGCGGUGAGGCCCCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGCGUCCCCUUCCCCGCCGGCCGCCUUUCUCGCG', '-structureDBN', '(((((..((((((((((.((.((((((.((((((((((((.((..(((((((((((((((.(((((((((((((((.(((((((....))))..))).))))))).))).)))))..))))))))))).))))..)))))))))))))).)))))).))))))).))))).....)))))', '-o', '/disk1/www/rails/humanrnamap/public/result/b9ea3d8d-07a1-4469-bb29-7b404a74680c/final_image/MIR3648_1_1_181_fold_1.svg', '-title', 'MIR3648-1-1-181, -193.1 ± 3.6\n kcal/mol, AUC: 0.993', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,4,7,8,10,11,13,14,16,17,18,19,20,21,22,23,24,25,26,27,29,32,34,35,36,37,39,41,44,46,47,48,51,52,53,55,56,59,64,65,66,67,68,71,73,75,76,77,78,81,84,85,87,88,90,91,92,93,95,96,101,103,105,106,107,108,109,110,114,115,117,118,120,121,122,124,125,128,130,132,134,136,137,138,139,140,145,146,147,148,150,151,156,157,162,165,166,169,172,173,174,176,178,180', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '1,3,131,133,9,12,141,142,15,143,144,149,152,153,154,155,30,31,158,33,159,160,161,163,38,164,40,167,42,43,168,170,49,50,54,57,58,60,62,63,69,70,72,74,79,80,82,83,89,97,98,99,100,102,104,111,112,113,119,123,126,127', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '177,5,6,175', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '129,135,171,45,179,116,86,28,61,94']
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Text: 'C', X: 356.8891951527951, Y: 46.580454482155005, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 375.0328907733465, Y: 54.99510297325594, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 393.17658639389765, Y: 63.40975146435687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 411.3202820144488, Y: 71.8243999554578, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 428.7455332285724, Y: 70.20865860094398, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 443.0911242584966, Y: 80.23133379283547, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 447.56780581441535, Y: 97.1490559281259, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 461.7099414381462, Y: 111.29119155185697, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 475.852077061877, Y: 125.4333271755878, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 489.9942126856081, Y: 139.57546279931864, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 504.13634830933916, Y: 153.7175984230497, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 518.27848393307, Y: 167.85973404678077, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 532.4206195568008, Y: 182.0018696705116, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 546.5627551805319, Y: 196.14400529424245, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 560.704890804263, Y: 210.2861409179735, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 574.8470264279938, Y: 224.42827654170458, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 588.9891620517246, Y: 238.5704121654354, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 603.7639133177349, Y: 247.94906473987646, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 605.9629883390819, Y: 265.3104145760793, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 612.7418648161481, Y: 284.1265468489106, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 619.5207412932143, Y: 302.9426791217419, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 626.2996177702807, Y: 321.75881139457294, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 640.8404186046241, Y: 331.49611651950124, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 646.771938790069, Y: 347.96023108086354, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 641.7821990369262, Y: 364.73379650971344, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 648.5610829837337, Y: 383.5499260914236, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 657.9396716073359, Y: 398.32463676301506, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 672.0818072310669, Y: 412.466772386746, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 686.2239428547978, Y: 426.60890801047697, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 700.3660784785288, Y: 440.7510436342079, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 714.5082141022597, Y: 454.89317925793887, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 728.6503497259907, Y: 469.0353148816698, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 742.7924853497216, Y: 483.17745050540077, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 756.9346209734526, Y: 497.3195861291317, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 771.0767565971835, Y: 511.4617217528627, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 785.2188922209145, Y: 525.6038573765936, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 799.3610278446454, Y: 539.7459930003246, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 813.5031634683764, Y: 553.8881286240555, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 829.6633207385573, Y: 560.6036343519578, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 836.3788264664595, Y: 576.7637916221387, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 850.5209620901906, Y: 590.9059272458696, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 864.6630977139214, Y: 605.0480628696006, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 878.8052333376523, Y: 619.1901984933315, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 892.9473689613833, Y: 633.3323341170625, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 907.0895045851142, Y: 647.4744697407934, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 923.2496618552952, Y: 654.1899754686957, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 929.9651675831974, Y: 670.3501327388766, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 944.1073032069283, Y: 684.4922683626075, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 958.8820906928946, Y: 693.8709779969723, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 977.698173016498, Y: 700.6499931165438, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 996.5142553401015, Y: 707.4290082361152, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 1015.330337663705, Y: 714.2080233556868, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 1034.1464199873083, Y: 720.9870384752583, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 1051.5076896689316, Y: 723.1862008253242, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 1060.8862782925337, Y: 737.9609114969159, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 1075.0284139162645, Y: 752.1030471206467, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 1089.1705495399956, Y: 766.2451827443778, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 1103.3126851637267, Y: 780.3873183681086, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 1117.4548207874575, Y: 794.5294539918397, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 1135.2040419998866, Y: 793.3119796471137, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 1151.3742923221957, Y: 800.7308813139151, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 1162.0276955268346, Y: 814.9794636148739, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 1164.5698710454226, Y: 832.5878264308911, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 1158.3817330665852, Y: 849.2678757648314, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 1144.9702540214203, Y: 860.9575860798438, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 1144.9702540214203, Y: 880.9575860798438, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 1144.9702540214203, Y: 900.9575860798438, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 1144.9702540214203, Y: 920.9575860798438, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 1144.9702540214203, Y: 940.9575860798438, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 1113.2202540214203, Y: 960.9575860798438, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 1048.297443527702, Y: 803.3682887566716, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 885.2751080919647, Y: 702.132871052258, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 758.4879218323515, Y: 576.8690990126183, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 615.6007785081761, Y: 433.8113157944349, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 542.4167318379841, Y: 264.06464179368106, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 407.9890510047685, Y: 135.45759740506912, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 242.69552880121097, Y: 87.19235392913322, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 81.50503565647946, Y: 167.63187620168014, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '90', X: -1.7973010966176943, Y: 182.1539338355417, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '100', X: 129.72132104033588, Y: 62.72253917426849, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '110', X: 320.9692368199993, Y: 8.0, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '120', X: 481.744212685608, Y: 111.29119155185685, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '130', X: 615.6720954022957, Y: 256.5086832979712, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '140', X: 692.1160784785286, Y: 412.4667723867459, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '150', X: 835.5554563622883, Y: 546.4614987282268, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '160', X: 957.4111058124661, Y: 675.054895673369, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '170', X: 1118.4956098095472, Y: 776.8184054811778, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '180', X: 1136.7202540214203, Y: 960.9575860798438, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'MIR3648-1-1-181, -193.1 ± 3.6
 kcal/mol, AUC: 0.993', X: 485.6599355227113, Y: 973.7575860798438, Width: 208.5, Height: 23
Calculated bounding box: (-1.7973010966176943, 0.0, 1175.0698710454226, 973.7575860798438)
Updated viewBox: -6.797301096617694 -5.0 1186.8671721420403 983.7575860798438
Updated SVG: /disk1/www/rails/humanrnamap/public/result/b9ea3d8d-07a1-4469-bb29-7b404a74680c/final_image/MIR3648_1_1_181_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/b9ea3d8d-07a1-4469-bb29-7b404a74680c/final_image/MIR3648_1_1_181_fold_final_1.svg
