Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  5% [===                                               ] -                     
 10% [======                                            ] \                     
 15% [========                                          ] |                     
 20% [===========                                       ] /                     
 26% [==============                                    ] -                     
 31% [================                                  ] \                     
 36% [===================                               ] |                     
 41% [=====================                             ] /                     
 46% [========================                          ] -                     
 52% [===========================                       ] \                     
 57% [=============================                     ] |                     
 62% [================================                  ] /                     
 67% [==================================                ] -                     
 72% [=====================================             ] \                     
 78% [========================================          ] |                     
 83% [==========================================        ] /                     
 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/184870c1-c726-419a-90e3-6299d469397c/final_image/KRAS_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 156.59 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 156.59 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 156.59 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 170.12 MB
Based on canonical annotations, the following gene is in your area of interest: KRAS(-)
write fasta - Elapsed time since the previous call: 0.54 seconds
write fasta - Current memory usage: 170.12 MB
Length of region: 96 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: 0.19 seconds
write dat - Current memory usage: 173.36 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/184870c1-c726-419a-90e3-6299d469397c/fasta/KRAS.fasta" "/disk1/www/rails/humanrnamap/public/result/184870c1-c726-419a-90e3-6299d469397c/ct/KRAS.ct" --SHAPE "KRAS.dat"

fold - Elapsed time since the previous call: 0.12 seconds
fold - Current memory usage: 173.36 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/184870c1-c726-419a-90e3-6299d469397c/ct/KRAS.ct" "/disk1/www/rails/humanrnamap/public/result/184870c1-c726-419a-90e3-6299d469397c/fold_FE/KRAS.txt" -sh "KRAS.dat"

efn2 - Elapsed time since the previous call: 0.49 seconds
efn2 - Current memory usage: 173.36 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/184870c1-c726-419a-90e3-6299d469397c/ct/KRAS.ct" 1 "/disk1/www/rails/humanrnamap/public/result/184870c1-c726-419a-90e3-6299d469397c/fold_dbn/KRAS_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 173.36 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AGAGAUUUUAAAGGGGGAGAAUUCUAGAAAUAAAUGUUACCUAAUUAUUACAGCCUUAAAGACAAAAAUCCUUGUUGAAGUUUUUUUAAAAAAAGC', '-structureDBN', '.......((((.((..........(((.............)))..........)))))).(((((......)))))...(((((((...)))))))', '-o', '/disk1/www/rails/humanrnamap/public/result/184870c1-c726-419a-90e3-6299d469397c/final_image/KRAS_fold_1.svg', '-title', 'KRAS, -8.0 ± 1.0\n kcal/mol, AUC: 0.701', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,4,6,7,8,9,13,14,15,16,17,19,22,23,25,27,31,35,36,37,38,42,45,46,48,49,53,56,57,61,69,72,73,74,75,76,77,80,81,82,83,84,85,86,87,95', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '32,64,41,10,18,50,88,89,90,91,92,94', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '96,1,34,65,66,67,68,39,43,47,79,26,28,93,63', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '3,5,70,71,11,12,78,20,21,24,29,30,33,40,44,51,52,54,55,58,59,60,62']
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 4.75, Y: 360.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 22.25, Y: 360.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 39.75, Y: 360.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 57.25, Y: 360.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 74.75, Y: 360.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 92.25, Y: 360.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 109.75, Y: 360.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 127.25, Y: 360.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 127.25, Y: 340.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 127.25, Y: 320.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 127.25, Y: 300.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 123.43438113341733, Y: 282.930860239896, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 134.15572209255677, Y: 269.0995509068937, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 142.66734010780456, Y: 251.00114327631715, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 130.34718764708822, Y: 238.57287829253872, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 121.39635938125025, Y: 223.53523883290993, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 116.34565926030007, Y: 206.77999023879644, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 115.49460499309004, Y: 189.30075587923218, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 118.89366598348875, Y: 172.1340930833986, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 126.34127038289836, Y: 156.29802299413078, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 137.3957587475328, Y: 142.73165965834804, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 151.40157542209283, Y: 132.23951848311964, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 167.52814444274964, Y: 125.44380668932638, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 184.81912453224547, Y: 122.74752504473395, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 202.2491222567605, Y: 124.31056902546834, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 210.7606576218228, Y: 106.21212252502812, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 219.2721929868851, Y: 88.11367602458802, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 209.97591963971982, Y: 73.2870613623545, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 207.10867830669676, Y: 56.02357018513942, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 211.11303944392373, Y: 38.9878931404711, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 221.37091349105862, Y: 24.809556830427823, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 236.29895552925927, Y: 15.677045598938093, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 253.59296106148872, Y: 13.0, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 270.58352942440644, Y: 17.19163299831871, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 284.6480967259182, Y: 27.604948853934502, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 293.61573933504195, Y: 42.632609567518784, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 296.1022648456412, Y: 59.95503409102912, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 291.7238678498226, Y: 76.89843517329655, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 281.1563718763357, Y: 90.84752938539202, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 266.0309132578771, Y: 99.6492168411512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 248.6821685501003, Y: 101.94492099281433, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 240.170633185038, Y: 120.04336749325444, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 231.65909781997567, Y: 138.14181399369448, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 243.97934357170618, Y: 150.57006988971492, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 252.9302520730472, Y: 165.60773051231908, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 257.98101102306975, Y: 182.36302322921208, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 258.8320971969195, Y: 199.84231532942826, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 255.43303895697846, Y: 217.00903904368099, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 247.98540935307335, Y: 232.84516272604205, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 236.93087231305276, Y: 246.41156279499225, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 222.9249908159191, Y: 256.90371621973054, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 206.79835029139915, Y: 263.6994108415414, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 189.5073027301083, Y: 266.3956441832938, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 172.07725250749135, Y: 264.8325225510948, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 163.56563449224356, Y: 282.93093018167133, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 159.75, Y: 300.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 159.75, Y: 320.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 159.75, Y: 340.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 159.75, Y: 360.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 177.25, Y: 360.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 194.75, Y: 360.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 194.75, Y: 340.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 194.75, Y: 320.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 194.75, Y: 300.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 194.75, Y: 280.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 185.90309990849715, Y: 264.9108352887463, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 188.8683050233931, Y: 247.66390192522718, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 202.2500121168788, Y: 236.38653223707618, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 219.7499878831212, Y: 236.38653223707618, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 233.1316949766069, Y: 247.66390192522724, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 236.09690009150285, Y: 264.9108352887463, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 227.25, Y: 280.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 227.25, Y: 300.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 227.25, Y: 320.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 227.25, Y: 340.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 227.25, Y: 360.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 244.75, Y: 360.00989190133106, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 262.25, Y: 360.00989190133106, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 279.75, Y: 360.00989190133106, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 297.25, Y: 360.00989190133106, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 297.25, Y: 340.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 297.25, Y: 320.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 297.25, Y: 300.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 297.25, Y: 280.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 297.25, Y: 260.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 297.25, Y: 240.00989190133103, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 298.19020113855714, Y: 222.5351440144096, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 313.5, Y: 214.0580660559045, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 328.80979886144286, Y: 222.5351440144096, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 329.75, Y: 240.00989190133103, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 329.75, Y: 260.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 329.75, Y: 280.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 329.75, Y: 300.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 329.75, Y: 320.009891901331, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 329.75, Y: 340.00989190133106, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 329.75, Y: 360.00989190133106, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 5.5, Y: 380.009891901331, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 103.5, Y: 320.009891901331, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 105.66387543697917, Y: 145.64610765721275, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 189.1720015148466, Y: 30.6760859324761, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 268.74829921527976, Y: 118.57467374126304, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 247.03167416489532, Y: 260.83915053726554, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 173.5, Y: 380.009891901331, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 246.73414637776455, Y: 237.71943460060584, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 279.35786437626905, Y: 374.152027525062, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '90', X: 345.22267446459404, Y: 234.48822671515356, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '96', X: 326.0, Y: 380.00989190133106, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'KRAS, -8.0 ± 1.0
 kcal/mol, AUC: 0.701', X: 101.25, Y: 392.80989190133107, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 363.22267446459404, 392.80989190133107)
Updated viewBox: -0.25 0.0 368.47267446459404 397.80989190133107
Updated SVG: /disk1/www/rails/humanrnamap/public/result/184870c1-c726-419a-90e3-6299d469397c/final_image/KRAS_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/184870c1-c726-419a-90e3-6299d469397c/final_image/KRAS_fold_final_1.svg
