Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  5% [===                                               ] -                     
 11% [======                                            ] \                     
 16% [=========                                         ] |                     
 22% [============                                      ] /                     
 28% [===============                                   ] -                     
 33% [=================                                 ] \                     
 39% [====================                              ] |                     
 44% [=======================                           ] /                     
 50% [==========================                        ] -                     
 56% [=============================                     ] \                     
 61% [===============================                   ] |                     
 67% [==================================                ] /                     
 73% [=====================================             ] -                     
 78% [========================================          ] \                     
 84% [===========================================       ] |                     
 89% [=============================================     ] /                     
 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/8d1a6494-20d1-4a5a-923f-069f0bea8177/final_image/TFRC_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.51 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.51 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.51 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 173.16 MB
Based on canonical annotations, the following gene is in your area of interest: TFRC(-)
write fasta - Elapsed time since the previous call: 0.60 seconds
write fasta - Current memory usage: 173.16 MB
Length of region: 89 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: 176.86 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/8d1a6494-20d1-4a5a-923f-069f0bea8177/fasta/TFRC.fasta" "/disk1/www/rails/humanrnamap/public/result/8d1a6494-20d1-4a5a-923f-069f0bea8177/ct/TFRC.ct" --SHAPE "TFRC.dat"

fold - Elapsed time since the previous call: 0.10 seconds
fold - Current memory usage: 176.86 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/8d1a6494-20d1-4a5a-923f-069f0bea8177/ct/TFRC.ct" "/disk1/www/rails/humanrnamap/public/result/8d1a6494-20d1-4a5a-923f-069f0bea8177/fold_FE/TFRC.txt" -sh "TFRC.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 176.86 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/8d1a6494-20d1-4a5a-923f-069f0bea8177/ct/TFRC.ct" 1 "/disk1/www/rails/humanrnamap/public/result/8d1a6494-20d1-4a5a-923f-069f0bea8177/fold_dbn/TFRC_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.03 seconds
ct2dot - Current memory usage: 176.86 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CGGCUCUCACACGCUGCCAGCUUUACUGGAGAACUUGAAACUGCGUAAACAAAAUAACGGUGCUUUUAAUGAAACGCUGUUCAGAAACC', '-structureDBN', '((((........))))((((.....))))..........................(((((((.(((....))).)))))))........', '-o', '/disk1/www/rails/humanrnamap/public/result/8d1a6494-20d1-4a5a-923f-069f0bea8177/final_image/TFRC_fold_1.svg', '-title', 'TFRC, -16.4 ± 0.6\n kcal/mol, AUC: 0.637', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,5,7,13,15,16,20,22,23,24,27,28,29,31,35,36,37,42,43,45,46,55,59,60,61,62,64,65,66,67,70,71,76,78,79,80,81,84', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '18,51,4,19,52,73,58', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '68,6,72,9,74,11,85,86,87,25,30,33,38,39,40,49,53,54,56,57,63', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,69,8,10,75,12,77,14,17,82,83,21,88,89,26,32,34,41,44,47,48,50']
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 19.088210690548294, Y: 236.05870447429055, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 19.088210690548294, Y: 216.05870447429055, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 19.088210690548294, Y: 196.05870447429055, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 19.088210690548294, Y: 176.05870447429055, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 7.433142616264604, Y: 163.00459028611044, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 4.75, Y: 145.71149181432065, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 11.901456083843698, Y: 129.73941665374466, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 26.588203418347973, Y: 120.22364228763743, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 44.088217962748615, Y: 120.22364228763743, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 58.77496529725295, Y: 129.73941665374466, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 65.92642138109659, Y: 145.71149181432065, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 63.243278764831985, Y: 163.00459028611044, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 51.588210690548294, Y: 176.05870447429055, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 51.588210690548294, Y: 196.05870447429055, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 51.588210690548294, Y: 216.05870447429055, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 51.588210690548294, Y: 236.05870447429055, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 69.0882106905483, Y: 236.05870447429055, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 69.0882106905483, Y: 216.05870447429055, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 69.0882106905483, Y: 196.05870447429055, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 69.0882106905483, Y: 176.05870447429055, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 62.4400410857304, Y: 159.87066417463598, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 69.16626034176983, Y: 143.71489794838254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 85.3382106905483, Y: 137.0276840476381, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 101.51016103932682, Y: 143.71489794838254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 108.23638029536619, Y: 159.87066417463598, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 101.5882106905483, Y: 176.05870447429055, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 101.5882106905483, Y: 196.05870447429055, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 101.5882106905483, Y: 216.05870447429055, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 101.5882106905483, Y: 236.05870447429055, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 119.0882106905483, Y: 236.05870447429055, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 136.5882106905483, Y: 236.05870447429058, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 154.0882106905483, Y: 236.05870447429058, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 171.5882106905483, Y: 236.05870447429058, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 189.0882106905483, Y: 236.05870447429058, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 206.5882106905483, Y: 236.05870447429058, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 224.0882106905483, Y: 236.05870447429058, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 241.5882106905483, Y: 236.05870447429058, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 259.0882106905483, Y: 236.05870447429058, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 276.5882106905483, Y: 236.05870447429058, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 294.0882106905483, Y: 236.05870447429058, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 311.5882106905483, Y: 236.05870447429058, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 329.0882106905483, Y: 236.05870447429058, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 346.5882106905483, Y: 236.05870447429058, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 364.0882106905483, Y: 236.05870447429058, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 381.5882106905483, Y: 236.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 399.0882106905483, Y: 236.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 416.5882106905483, Y: 236.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 434.0882106905483, Y: 236.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 451.5882106905483, Y: 236.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 469.0882106905483, Y: 236.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 486.5882106905483, Y: 236.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 504.0882106905483, Y: 236.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 521.5882106905483, Y: 236.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 539.0882106905483, Y: 236.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 556.5882106905483, Y: 236.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 574.0882106905483, Y: 236.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 574.0882106905483, Y: 216.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 574.0882106905483, Y: 196.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 574.0882106905483, Y: 176.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 574.0882106905483, Y: 156.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 574.0882106905483, Y: 136.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 574.0882106905483, Y: 116.05870447429058, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 567.409833539059, Y: 99.88316804420785, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 574.0882106905483, Y: 83.70763161412506, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 574.0882106905483, Y: 63.70763161412506, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 574.0882106905483, Y: 43.70763161412506, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 570.5394763033092, Y: 26.571186946533857, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 581.5881928106153, Y: 13.000000000000114, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 599.0882285704813, Y: 13.0, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 610.1369450777873, Y: 26.5711869465338, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 606.5882106905483, Y: 43.70763161412506, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 606.5882106905483, Y: 63.70763161412506, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 606.5882106905483, Y: 83.70763161412506, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 613.2665878420376, Y: 99.88316804420785, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 606.5882106905483, Y: 116.05870447429058, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 606.5882106905483, Y: 136.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 606.5882106905483, Y: 156.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 606.5882106905483, Y: 176.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 606.5882106905483, Y: 196.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 606.5882106905483, Y: 216.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 606.5882106905483, Y: 236.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 624.0882106905483, Y: 236.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 641.5882106905483, Y: 236.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 659.0882106905483, Y: 236.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 676.5882106905483, Y: 236.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 694.0882106905483, Y: 236.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 711.5882106905483, Y: 236.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 729.0882106905483, Y: 236.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 746.5882106905483, Y: 236.0587044742906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 19.838210690548294, Y: 256.05870447429055, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 70.21260703511093, Y: 116.72651772835243, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 45.338225248421836, Y: 176.03457327602737, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 115.3382106905483, Y: 256.05870447429055, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 290.3382106905483, Y: 256.0587044742906, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 465.3382106905483, Y: 256.0587044742906, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 550.3382106905483, Y: 156.0587044742906, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 625.8158483305176, Y: 21.8259031408962, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 622.8382106905483, Y: 216.0587044742906, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '89', X: 742.8382106905483, Y: 256.0587044742906, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'TFRC, -16.4 ± 0.6
 kcal/mol, AUC: 0.637', X: 309.66910534527415, Y: 268.8587044742906, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 760.8382106905483, 268.8587044742906)
Updated viewBox: -0.25 0.0 766.0882106905483 273.8587044742906
Updated SVG: /disk1/www/rails/humanrnamap/public/result/8d1a6494-20d1-4a5a-923f-069f0bea8177/final_image/TFRC_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/8d1a6494-20d1-4a5a-923f-069f0bea8177/final_image/TFRC_fold_final_1.svg
