Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  6% [====                                              ] -                     
 12% [=======                                           ] \                     
 18% [==========                                        ] |                     
 24% [=============                                     ] /                     
 30% [================                                  ] -                     
 36% [===================                               ] \                     
 42% [======================                            ] |                     
 48% [=========================                         ] /                     
 54% [============================                      ] -                     
 60% [===============================                   ] \                     
 67% [==================================                ] |                     
 73% [=====================================             ] /                     
 79% [========================================          ] -                     
 85% [===========================================       ] \                     
 91% [==============================================    ] |                     
 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/03b639a2-b6fd-4d9e-9c25-df63936bbc30/final_image/CHD2_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.17 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.17 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.17 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.89 MB
Based on canonical annotations, the following gene is in your area of interest: CHD2(+)
write fasta - Elapsed time since the previous call: 0.68 seconds
write fasta - Current memory usage: 172.89 MB
Length of region: 82 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: 176.56 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/03b639a2-b6fd-4d9e-9c25-df63936bbc30/fasta/CHD2.fasta" "/disk1/www/rails/humanrnamap/public/result/03b639a2-b6fd-4d9e-9c25-df63936bbc30/ct/CHD2.ct" --SHAPE "CHD2.dat"

fold - Elapsed time since the previous call: 0.11 seconds
fold - Current memory usage: 176.56 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/03b639a2-b6fd-4d9e-9c25-df63936bbc30/ct/CHD2.ct" "/disk1/www/rails/humanrnamap/public/result/03b639a2-b6fd-4d9e-9c25-df63936bbc30/fold_FE/CHD2.txt" -sh "CHD2.dat"

efn2 - Elapsed time since the previous call: 0.52 seconds
efn2 - Current memory usage: 176.56 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/03b639a2-b6fd-4d9e-9c25-df63936bbc30/ct/CHD2.ct" 1 "/disk1/www/rails/humanrnamap/public/result/03b639a2-b6fd-4d9e-9c25-df63936bbc30/fold_dbn/CHD2_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.56 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AACUGACAAAGCCAAAUUAAAGAAGCGGAAGCCUCGGGUAAAGAAGGAAAACAAAGUGCCCAGGCUGAAAGAGGAGCAUGGA', '-structureDBN', '...........(((...............(((((.(((((................))))))))))............))).', '-o', '/disk1/www/rails/humanrnamap/public/result/03b639a2-b6fd-4d9e-9c25-df63936bbc30/final_image/CHD2_fold_1.svg', '-title', 'CHD2, -17.3 ± 0.7\n kcal/mol, AUC: 0.873', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '4,5,11,17,18,22,25,27,28,31,34,36,37,38,39,43,46,47,56,57,58,63,64,66,67,71,73,74,76,79,80,81', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '32,33,40,9,72,14,48,82,62,59,30', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,65,68,7,8,10,75,13,16,19,23,29,35,49,51,60,61', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '2,3,69,6,70,12,77,78,15,20,21,24,26,41,42,44,45,50,52,53,54,55']
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 4.75, Y: 471.54553868333755, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 22.25, Y: 471.54553868333755, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 39.75, Y: 471.54553868333755, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 57.25, Y: 471.54553868333755, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 74.75, Y: 471.54553868333755, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 92.25, Y: 471.54553868333755, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 109.75, Y: 471.54553868333755, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 127.25, Y: 471.54553868333755, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 144.75, Y: 471.54553868333755, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 162.25, Y: 471.54553868333755, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 179.75, Y: 471.54553868333755, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 197.25, Y: 471.54553868333755, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 197.25, Y: 451.54553868333755, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 197.25, Y: 431.54553868333755, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 180.40727720987024, Y: 426.7945501995498, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 164.78047854836055, Y: 418.9172177734755, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 150.9437786358587, Y: 408.20297780558167, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 139.40557859096663, Y: 395.04550303713575, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 130.58982587562036, Y: 379.92823785390544, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 124.82043721636188, Y: 363.4066351151678, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 122.30939694952605, Y: 346.08774717925894, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 123.14896809220411, Y: 328.60792101151276, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 127.30830232718296, Y: 311.6094169220355, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 134.63457346100068, Y: 295.71681002977175, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 144.8585927085302, Y: 281.51404153259534, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 157.60469948199253, Y: 269.522962987371, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 172.40456426767219, Y: 260.1841619463464, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 188.71439643198045, Y: 253.8407734724835, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 205.93492469137567, Y: 250.7258723463463, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 223.43341610481298, Y: 250.95390921201005, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 229.1134892071529, Y: 231.77744526392837, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 234.7935623094928, Y: 212.60098131584675, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 240.47363541183273, Y: 193.42451736776513, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 246.15370851417265, Y: 174.24805341968352, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 247.6422310763627, Y: 156.27341364132337, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 262.7282700131113, Y: 146.3883337843439, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 276.87040563684224, Y: 132.24619816061295, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 291.0125412605732, Y: 118.104062536882, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 305.15467688430414, Y: 103.96192691315105, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 319.2968125080351, Y: 89.8197912894201, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 314.01989808466516, Y: 73.13435030996186, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 314.48371741826793, Y: 55.6405045882135, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 320.63736841122557, Y: 39.25812545795827, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 331.8055153867866, Y: 25.78510576514907, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 346.76250415942224, Y: 16.700049168418104, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 363.8668721004437, Y: 13.0, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 381.2414913207203, Y: 15.091022109149094, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 396.97957506181297, Y: 22.74363517064046, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 409.35393901537753, Y: 35.11799912420497, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 417.00655207686884, Y: 50.85608286529771, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 419.097574186018, Y: 68.2307020855742, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 415.3975250175999, Y: 85.33507002659564, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 406.31246842086887, Y: 100.29205879923131, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 392.83944872805984, Y: 111.46020577479237, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 376.45706959780455, Y: 117.61385676775001, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 358.9632238760562, Y: 118.07767610135284, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 342.2777828965979, Y: 112.8007616779829, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 328.13564727286695, Y: 126.94289730171386, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 313.993511649136, Y: 141.0850329254448, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 299.85137602540505, Y: 155.22716854917576, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 285.7092404016741, Y: 169.3693041729067, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 277.3154624298053, Y: 183.47817221098592, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 271.63538932746536, Y: 202.65463615906754, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 265.95531622512544, Y: 221.83110010714915, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 260.2752431227855, Y: 241.00756405523083, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 254.5951700204456, Y: 260.1840280033124, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 269.39508334225604, Y: 269.5227948205585, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 282.14124128376994, Y: 281.51385222722547, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 292.36531123171966, Y: 295.7166123005152, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 299.6916297572565, Y: 311.60922243423374, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 303.8510056329974, Y: 328.607739790883, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 304.6906107375283, Y: 346.08758713771203, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 302.1795954254483, Y: 363.40650171405014, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 296.4102220371787, Y: 379.9281339187304, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 287.5944748999373, Y: 395.0454287300457, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 276.0562713787558, Y: 408.2029307537505, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 262.2195601672157, Y: 418.9171933437956, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 246.59274412290478, Y: 426.79454190262334, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 229.75, Y: 431.54553868333755, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 229.75, Y: 451.54553868333755, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 229.75, Y: 471.54553868333755, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 247.25, Y: 471.5455386833376, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 5.5, Y: 491.54553868333755, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 158.5, Y: 491.54553868333755, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 101.64355785372935, Y: 368.16019780327053, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 207.06260464239313, Y: 235.4389126593178, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 296.5794738853665, Y: 83.47628551004038, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 432.44313966139634, Y: 45.210300646574126, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 310.243511649136, Y: 169.3693041729067, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 314.8234819090113, Y: 305.01561497554525, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 246.0, Y: 451.54553868333755, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '82', X: 243.5, Y: 491.5455386833376, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'CHD2, -17.3 ± 0.7
 kcal/mol, AUC: 0.873', X: 145.923787093009, Y: 504.3455386833376, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 450.44313966139634, 504.3455386833376)
Updated viewBox: -0.25 0.0 455.69313966139634 509.3455386833376
Updated SVG: /disk1/www/rails/humanrnamap/public/result/03b639a2-b6fd-4d9e-9c25-df63936bbc30/final_image/CHD2_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/03b639a2-b6fd-4d9e-9c25-df63936bbc30/final_image/CHD2_fold_final_1.svg
