Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  5% [===                                               ] -                     
 10% [======                                            ] \                     
 15% [========                                          ] |                     
 21% [===========                                       ] /                     
 26% [==============                                    ] -                     
 31% [================                                  ] \                     
 37% [===================                               ] |                     
 42% [======================                            ] /                     
 47% [========================                          ] -                     
 53% [===========================                       ] \                     
 58% [==============================                    ] |                     
 63% [================================                  ] /                     
 69% [===================================               ] -                     
 74% [======================================            ] \                     
 79% [========================================          ] |                     
 85% [===========================================       ] /                     
 90% [==============================================    ] -                     
 95% [================================================  ] \                     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/92cb70ac-1757-4a67-9898-51e6518a98cd/final_image/TFRC_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 155.92 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 155.92 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 155.92 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 169.39 MB
Based on canonical annotations, the following gene is in your area of interest: TFRC(-)
write fasta - Elapsed time since the previous call: 1.21 seconds
write fasta - Current memory usage: 169.39 MB
Length of region: 94 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: 172.44 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/92cb70ac-1757-4a67-9898-51e6518a98cd/fasta/TFRC.fasta" "/disk1/www/rails/humanrnamap/public/result/92cb70ac-1757-4a67-9898-51e6518a98cd/ct/TFRC.ct" --SHAPE "TFRC.dat"

fold - Elapsed time since the previous call: 0.10 seconds
fold - Current memory usage: 172.44 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/92cb70ac-1757-4a67-9898-51e6518a98cd/ct/TFRC.ct" "/disk1/www/rails/humanrnamap/public/result/92cb70ac-1757-4a67-9898-51e6518a98cd/fold_FE/TFRC.txt" -sh "TFRC.dat"

efn2 - Elapsed time since the previous call: 0.53 seconds
efn2 - Current memory usage: 172.44 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/92cb70ac-1757-4a67-9898-51e6518a98cd/ct/TFRC.ct" 1 "/disk1/www/rails/humanrnamap/public/result/92cb70ac-1757-4a67-9898-51e6518a98cd/fold_dbn/TFRC_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 172.44 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AUUGCCUAAUAUACCUGUCCAGACAAUCUCCAGAGCUGCUGCAGAAAAGCUGUUUGGGAAUAUGGAAGGAGACUGUCCCUCUGACUGGAAAACA', '-structureDBN', '.................(((((......(((.((((.(((.......))).)))).)))...((((.(((.....))).)))).))))).....', '-o', '/disk1/www/rails/humanrnamap/public/result/92cb70ac-1757-4a67-9898-51e6518a98cd/final_image/TFRC_fold_1.svg', '-title', 'TFRC, -15.7 ± 1.1\n kcal/mol, AUC: 0.531', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,4,7,10,12,16,17,18,22,27,29,33,35,37,38,40,41,44,49,51,52,53,54,55,56,57,58,61,63,64,65,68,69,71,74,75,76,80,82,83,86,87,88', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '1,21,70,6,90,78,15', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '9,13,77,84,23,25,26,89,28,92,30,31,32,94,34,46,47,48,59,60,62', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '66,67,5,8,72,73,11,14,79,81,19,20,85,24,91,93,36,39,42,43,45,50']
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 4.75, Y: 448.0108183676732, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 22.25, Y: 448.0108183676732, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 39.75, Y: 448.0108183676732, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 57.25, Y: 448.0108183676732, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 74.75, Y: 448.0108183676732, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 92.25, Y: 448.0108183676732, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 109.75, Y: 448.0108183676732, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 127.25, Y: 448.0108183676732, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 144.75, Y: 448.0108183676732, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 162.25, Y: 448.0108183676732, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 179.75, Y: 448.0108183676732, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 197.25, Y: 448.0108183676732, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 214.75, Y: 448.0108183676732, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 232.25, Y: 448.0108183676732, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 249.75, Y: 448.01081836767327, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 267.25, Y: 448.01081836767327, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 284.75, Y: 448.01081836767327, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 302.25, Y: 448.01081836767327, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 302.25, Y: 428.0108183676732, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 302.25, Y: 408.0108183676732, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 302.25, Y: 388.0108183676732, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 302.25, Y: 368.0108183676732, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 285.9014880920871, Y: 359.16526112070267, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 273.6929086931497, Y: 345.14854561126754, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 267.1747219863043, Y: 327.7407609541865, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 267.1747219863043, Y: 309.1526538796993, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 273.6929086931497, Y: 291.7448692226184, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 285.90148809208716, Y: 277.72815371318313, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 302.25, Y: 268.8825964662126, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 302.25, Y: 248.88259646621256, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 302.25, Y: 228.88259646621256, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 295.57162284851074, Y: 212.70706003612986, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 302.25, Y: 196.53152360604713, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 302.25, Y: 176.53152360604702, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 302.25, Y: 156.53152360604702, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 302.25, Y: 136.53152360604713, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 295.57162284851074, Y: 120.35598717596429, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 302.25, Y: 104.18045074588156, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 302.25, Y: 84.18045074588144, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 302.25, Y: 64.18045074588144, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 291.7979233435556, Y: 50.14462921679751, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 291.6508797232032, Y: 32.64524149601709, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 301.86561713592346, Y: 18.43576113895756, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 318.5, Y: 13.0, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 335.13438286407654, Y: 18.43576113895756, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 345.3491202767968, Y: 32.64524149601709, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 345.2020766564444, Y: 50.14462921679751, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 334.75, Y: 64.18045074588144, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 334.75, Y: 84.18045074588144, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 334.75, Y: 104.18045074588144, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 341.42837715148926, Y: 120.35598717596429, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 334.75, Y: 136.53152360604713, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 334.75, Y: 156.53152360604702, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 334.75, Y: 176.53152360604702, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 334.75, Y: 196.53152360604702, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 341.42837715148926, Y: 212.70706003612986, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 334.75, Y: 228.88259646621256, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 334.75, Y: 248.88259646621256, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 334.75, Y: 268.8825964662126, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 348.67282868947996, Y: 275.89951005669843, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 359.8998155810335, Y: 286.717874091516, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 367.4278667705887, Y: 300.3711037585357, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 370.58437594527425, Y: 315.63932843867053, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 389.89683855194886, Y: 320.8382502562971, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 409.20930115862353, Y: 326.03717207392356, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 428.5217637652982, Y: 331.2360938915501, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 445.877215124321, Y: 328.9920554596557, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 459.76066775290246, Y: 339.64555927150843, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 479.0731485801402, Y: 344.84441340463945, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 498.385629407378, Y: 350.0432675377705, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 515.7453335046478, Y: 347.83159814726446, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 529.5972981403602, Y: 358.5261707693303, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 531.8508521070717, Y: 375.88048730317234, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 521.1897370492065, Y: 389.7582188743128, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 503.8409091355336, Y: 392.05364429445297, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 489.9374914410401, Y: 381.42604888203186, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 470.6250106138023, Y: 376.22719474890084, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 451.31252978656454, Y: 371.0283406157698, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 433.95700869752005, Y: 373.27241898510783, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 420.0735158116551, Y: 362.61884562739647, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 400.76105320498044, Y: 357.4199238097699, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 381.44859059830577, Y: 352.22100199214333, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 362.1361279916311, Y: 347.0220801745169, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 350.22883332542693, Y: 359.8465229979764, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 334.75, Y: 368.0108183676732, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 334.75, Y: 388.0108183676732, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 334.75, Y: 408.0108183676732, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 334.75, Y: 428.01081836767327, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 334.75, Y: 448.01081836767327, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 352.25, Y: 448.01081836767327, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 369.75, Y: 448.01081836767327, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 387.25, Y: 448.01081836767327, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 404.75, Y: 448.01081836767327, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 422.25, Y: 448.01081836767327, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 5.5, Y: 468.0108183676732, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 158.5, Y: 468.0108183676732, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 278.5, Y: 408.0108183676732, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 278.5, Y: 248.88259646621256, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 278.76225761791295, Y: 67.40868953171582, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 351.0, Y: 104.18045074588144, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 356.492169107858, Y: 259.58539462607564, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 499.8577814214874, Y: 330.7370734969572, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 411.12461091514706, Y: 381.93131278923425, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '90', X: 348.5, Y: 468.01081836767327, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '94', X: 418.5, Y: 468.01081836767327, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'TFRC, -15.7 ± 1.1
 kcal/mol, AUC: 0.531', X: 202.30042605353583, Y: 480.8108183676733, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 542.3508521070717, 480.8108183676733)
Updated viewBox: -0.25 0.0 547.6008521070717 485.8108183676733
Updated SVG: /disk1/www/rails/humanrnamap/public/result/92cb70ac-1757-4a67-9898-51e6518a98cd/final_image/TFRC_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/92cb70ac-1757-4a67-9898-51e6518a98cd/final_image/TFRC_fold_final_1.svg
