Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  4% [===                                               ] -                     
  9% [=====                                             ] \                     
 14% [========                                          ] |                     
 19% [==========                                        ] /                     
 24% [=============                                     ] -                     
 29% [===============                                   ] \                     
 34% [==================                                ] |                     
 39% [====================                              ] /                     
 44% [=======================                           ] -                     
 49% [=========================                         ] \                     
 54% [============================                      ] |                     
 59% [==============================                    ] /                     
 64% [=================================                 ] -                     
 69% [===================================               ] \                     
 74% [======================================            ] |                     
 79% [========================================          ] /                     
 84% [===========================================       ] -                     
 89% [=============================================     ] \                     
 94% [================================================  ] |                     
 99% [==================================================] /                     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/c1dee1e2-e5ad-46a9-9350-9e1b70941dd0/final_image/ITCH_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.94 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.94 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.94 MB
read annotations - Elapsed time since the previous call: 0.10 seconds
read annotations - Current memory usage: 172.55 MB
Based on canonical annotations, the following gene is in your area of interest: ITCH(+)
write fasta - Elapsed time since the previous call: 0.30 seconds
write fasta - Current memory usage: 172.55 MB
Length of region: 101 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: 0.18 seconds
write dat - Current memory usage: 176.09 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/c1dee1e2-e5ad-46a9-9350-9e1b70941dd0/fasta/ITCH.fasta" "/disk1/www/rails/humanrnamap/public/result/c1dee1e2-e5ad-46a9-9350-9e1b70941dd0/ct/ITCH.ct" --SHAPE "ITCH.dat"

fold - Elapsed time since the previous call: 0.13 seconds
fold - Current memory usage: 176.09 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/c1dee1e2-e5ad-46a9-9350-9e1b70941dd0/ct/ITCH.ct" "/disk1/www/rails/humanrnamap/public/result/c1dee1e2-e5ad-46a9-9350-9e1b70941dd0/fold_FE/ITCH.txt" -sh "ITCH.dat"

efn2 - Elapsed time since the previous call: 0.45 seconds
efn2 - Current memory usage: 176.09 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/c1dee1e2-e5ad-46a9-9350-9e1b70941dd0/ct/ITCH.ct" 1 "/disk1/www/rails/humanrnamap/public/result/c1dee1e2-e5ad-46a9-9350-9e1b70941dd0/fold_dbn/ITCH_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.09 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AAGUCUGAUUGUUUCAGUUGCCUGACAAAUACUACACUUUACAAACAAUGUUAACACUGUGAUUCCUUCAUUGUUUUAAGAAGUUAACCUAGGGCCGGGCA', '-structureDBN', '....((((.....)))).((((((...........(((((..((((((((..................))))))))...)))))...........))))))', '-o', '/disk1/www/rails/humanrnamap/public/result/c1dee1e2-e5ad-46a9-9350-9e1b70941dd0/final_image/ITCH_fold_1.svg', '-title', 'ITCH, -17.5 ± 1.0\n kcal/mol, AUC: 0.621', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,4,6,7,9,10,11,12,13,14,17,18,19,20,23,24,30,33,38,39,40,49,50,51,52,58,59,60,61,63,64,67,68,71,72,73,74,75,76,77,80,83,84,85,90,92,93,94,97,98,99', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '96,1,2,100,5,101,95', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '66,69,70,45,46,47,16,78,22,86,87,27,28,31', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '65,8,15,79,81,82,21,88,25,26,89,91,29,32,34,35,36,37,41,42,43,44,48,53,54,55,56,57,62']
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 4.75, Y: 655.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 22.25, Y: 655.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 39.75, Y: 655.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 57.25, Y: 655.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 74.75, Y: 655.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 74.75, Y: 635.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 74.75, Y: 615.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 74.75, Y: 595.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 68.10183039518209, Y: 579.6492428563686, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 74.82804965122152, Y: 563.4934766301152, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 91.0, Y: 556.8062627293707, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 107.1719503487785, Y: 563.4934766301152, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 113.8981696048179, Y: 579.6492428563686, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 107.25, Y: 595.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 107.25, Y: 615.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 107.25, Y: 635.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 107.25, Y: 655.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 124.75, Y: 655.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 142.25, Y: 655.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 142.25, Y: 635.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 142.25, Y: 615.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 142.25, Y: 595.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 142.25, Y: 575.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 142.25, Y: 555.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 125.66483723564428, Y: 550.2532408820739, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 110.7577502432315, Y: 541.0865670339399, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 98.29058149303461, Y: 528.805734187934, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 88.90047884920673, Y: 514.0383673144593, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 83.06733345331914, Y: 497.5391683391193, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 81.08925437927246, Y: 480.1513463014332, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 83.06733345331914, Y: 462.76352426374706, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 88.90047884920676, Y: 446.2643252884071, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 98.29058149303464, Y: 431.49695841493235, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 110.75775024323153, Y: 419.2161255689264, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 125.66483723564431, Y: 410.0494517207926, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 142.25, Y: 404.4654094468432, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 142.25, Y: 384.4654094468432, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 142.25, Y: 364.4654094468432, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 142.25, Y: 344.4654094468432, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 142.25, Y: 324.4654094468432, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 130.6688475784504, Y: 311.3457513758174, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 128.1464749042966, Y: 294.0285300223645, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 135.50389068569098, Y: 278.1503389310757, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 129.79865677535165, Y: 258.9813455817025, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 124.09342286501231, Y: 239.81235223232932, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 118.38818895467298, Y: 220.64335888295614, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 112.68295504433365, Y: 201.47436553358295, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 106.9777211339943, Y: 182.30537218420977, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 101.27248722365495, Y: 163.1363788348366, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 95.5672533133156, Y: 143.9673854854634, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 78.24682984648508, Y: 141.46674188284987, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 62.446443672154516, Y: 133.9435720562642, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 49.586775598200816, Y: 122.07431662361978, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 40.82409379596878, Y: 106.92619148779988, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 36.946288746400455, Y: 89.86122985598934, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 38.30203061172014, Y: 72.41381596474912, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 44.769418798661064, Y: 56.15272198134676, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 55.7669425660994, Y: 42.54005293805278, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 70.3057671616319, Y: 32.79978256819322, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 87.078644215246, Y: 27.807700553445102, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 104.57745207345562, Y: 28.012666499608713, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 121.22879751595622, Y: 33.396251035226214, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 135.53548632012038, Y: 43.47439287578527, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 146.2111424452558, Y: 57.340922859724515, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 152.29587164566908, Y: 73.74904152260785, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 153.2425696986672, Y: 91.22342420967504, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 148.96611490279878, Y: 108.19287387301176, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 139.8510217368373, Y: 123.13159416872213, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 126.71686750604707, Y: 134.69638038116204, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 132.4221014163864, Y: 153.8653737305351, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 138.12733532672576, Y: 173.0343670799084, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 143.8325692370651, Y: 192.20336042928147, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 149.53780314740445, Y: 211.37235377865477, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 155.24303705774378, Y: 230.54134712802784, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 160.9482709680831, Y: 249.71034047740113, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 166.65350487842244, Y: 268.8793338267742, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 181.49602168242683, Y: 278.15023965753574, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 188.85351237168118, Y: 294.02844266535544, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 186.33117097893486, Y: 311.34571132696715, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 174.75, Y: 324.4654094468432, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 174.75, Y: 344.4654094468432, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 174.75, Y: 364.4654094468432, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 174.75, Y: 384.4654094468432, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 174.74999999999997, Y: 404.4654094468432, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 191.3351627643557, Y: 410.0494517207925, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 206.2422497567685, Y: 419.2161255689264, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 218.7094185069654, Y: 431.49695841493235, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 228.09952115079324, Y: 446.2643252884071, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 233.93266654668085, Y: 462.76352426374706, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 235.91074562072754, Y: 480.15134630143314, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 233.93266654668088, Y: 497.5391683391192, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 228.09952115079324, Y: 514.0383673144593, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 218.70941850696542, Y: 528.805734187934, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 206.24224975676847, Y: 541.08656703394, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 191.33516276435572, Y: 550.2532408820739, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 174.75, Y: 555.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 174.75, Y: 575.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 174.75, Y: 595.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 174.75, Y: 615.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 174.75, Y: 635.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 174.75, Y: 655.8372831560232, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 5.5, Y: 675.8372831560232, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 56.952987655391624, Y: 549.3342879664253, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 118.5, Y: 635.8372831560232, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 57.33925437927246, Y: 480.1513463014332, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 118.96886491441208, Y: 328.77061121546177, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 77.64261952125214, Y: 158.07694808892109, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 80.56187736835561, Y: 8.0, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 147.84109476575958, Y: 148.1601398201957, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 190.5311381831608, Y: 328.77059716287584, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '90', X: 252.16074562072754, Y: 480.15134630143314, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '100', X: 186.5, Y: 635.8372831560232, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '101', X: 166.5, Y: 675.8372831560232, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'ITCH, -17.5 ± 1.0
 kcal/mol, AUC: 0.621', X: 54.33037281036377, Y: 688.6372831560232, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 270.16074562072754, 688.6372831560232)
Updated viewBox: -0.25 -5.0 275.41074562072754 698.6372831560232
Updated SVG: /disk1/www/rails/humanrnamap/public/result/c1dee1e2-e5ad-46a9-9350-9e1b70941dd0/final_image/ITCH_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/c1dee1e2-e5ad-46a9-9350-9e1b70941dd0/final_image/ITCH_fold_final_1.svg
