Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  6% [====                                              ] -                     
 12% [=======                                           ] \                     
 18% [==========                                        ] |                     
 24% [=============                                     ] /                     
 30% [================                                  ] -                     
 37% [===================                               ] \                     
 43% [======================                            ] |                     
 49% [=========================                         ] /                     
 55% [============================                      ] -                     
 61% [===============================                   ] \                     
 67% [==================================                ] |                     
 74% [======================================            ] /                     
 80% [=========================================         ] -                     
 86% [============================================      ] \                     
 92% [===============================================   ] |                     
 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/aa090649-b7de-4c56-ad84-21d96f1e7805/final_image/BCOR_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.38 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.38 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.38 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.02 MB
Based on canonical annotations, the following gene is in your area of interest: BCOR(-)
write fasta - Elapsed time since the previous call: 0.25 seconds
write fasta - Current memory usage: 172.02 MB
Length of region: 81 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: 175.18 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/aa090649-b7de-4c56-ad84-21d96f1e7805/fasta/BCOR.fasta" "/disk1/www/rails/humanrnamap/public/result/aa090649-b7de-4c56-ad84-21d96f1e7805/ct/BCOR.ct" --SHAPE "BCOR.dat"

fold - Elapsed time since the previous call: 0.09 seconds
fold - Current memory usage: 175.18 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/aa090649-b7de-4c56-ad84-21d96f1e7805/ct/BCOR.ct" "/disk1/www/rails/humanrnamap/public/result/aa090649-b7de-4c56-ad84-21d96f1e7805/fold_FE/BCOR.txt" -sh "BCOR.dat"

efn2 - Elapsed time since the previous call: 0.44 seconds
efn2 - Current memory usage: 175.18 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/aa090649-b7de-4c56-ad84-21d96f1e7805/ct/BCOR.ct" 1 "/disk1/www/rails/humanrnamap/public/result/aa090649-b7de-4c56-ad84-21d96f1e7805/fold_dbn/BCOR_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.18 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AAACCGAAUACACCCGAGACAGUGGAGGCUUCUGCCGUCUCUGGAAAACCCCCAAAUGGCUUCAGUGCUAUAUACAAAACA', '-structureDBN', '............((.(((((.(((((....))))).))))).))...........(((((......)))))..........', '-o', '/disk1/www/rails/humanrnamap/public/result/aa090649-b7de-4c56-ad84-21d96f1e7805/final_image/BCOR_fold_1.svg', '-title', 'BCOR, -20.7 ± 0.7\n kcal/mol, AUC: 0.645', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '65,66,67,69,6,71,9,73,16,18,22,23,24,25,27,28,30,31,33,34,37,38,40,42,43,44,57,58,59,61,62', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '32,64,3,36,68,39,41,45,14,77,48,80,54,60', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '2,35,5,70,76,46,78,79,50,19,51,21,29', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,4,7,8,72,10,11,12,13,74,15,75,17,81,20,26,47,49,52,53,55,56,63']
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 4.75, Y: 288.40977733445595, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 22.25, Y: 288.40977733445595, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 39.75, Y: 288.40977733445595, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 57.25, Y: 288.40977733445595, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 74.75, Y: 288.40977733445595, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 92.25, Y: 288.40977733445595, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 109.75, Y: 288.40977733445595, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 127.25, Y: 288.40977733445595, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 144.75, Y: 288.40977733445595, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 162.25, Y: 288.40977733445595, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 179.75, Y: 288.40977733445595, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 197.25, Y: 288.40977733445595, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 214.75, Y: 288.40977733445595, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 214.75, Y: 268.40977733445595, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 208.07162284851074, Y: 252.23424090437322, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 214.75, Y: 236.05870447429047, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 214.75, Y: 216.05870447429047, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 214.75, Y: 196.05870447429047, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 214.75, Y: 176.05870447429047, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 214.75, Y: 156.05870447429047, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 208.07162284851074, Y: 139.88316804420768, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 214.75, Y: 123.70763161412495, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 214.75, Y: 103.70763161412495, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 214.75, Y: 83.70763161412495, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 214.75, Y: 63.70763161412498, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 214.75, Y: 43.70763161412492, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 211.2012656127609, Y: 26.57118694653377, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 222.24998212006702, Y: 13.0, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 239.75001787993295, Y: 13.0, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 250.7987343872391, Y: 26.57118694653377, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 247.25, Y: 43.70763161412492, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 247.25, Y: 63.70763161412498, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 247.25, Y: 83.70763161412495, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 247.25, Y: 103.70763161412495, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 247.25, Y: 123.70763161412495, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 253.92837715148926, Y: 139.88316804420768, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 247.25, Y: 156.05870447429047, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 247.25, Y: 176.05870447429047, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 247.25, Y: 196.05870447429047, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 247.25, Y: 216.05870447429047, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 247.25, Y: 236.05870447429047, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 253.92837715148926, Y: 252.23424090437322, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 247.25, Y: 268.40977733445595, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 247.25, Y: 288.40977733445595, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 264.75, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 282.25, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 299.75, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 317.25, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 334.75, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 352.25, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 369.75, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 387.25, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 404.75, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 422.25, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 439.75, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 457.25, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 457.25, Y: 268.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 457.25, Y: 248.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 457.25, Y: 228.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 457.25, Y: 208.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 448.40309990849715, Y: 193.31072072187123, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 451.36830502339313, Y: 176.06378735835216, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 464.7500121168788, Y: 164.78641767020113, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 482.2499878831212, Y: 164.78641767020113, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 495.6316949766069, Y: 176.06378735835216, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 498.5969000915029, Y: 193.31072072187126, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 489.75, Y: 208.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 489.75, Y: 228.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 489.75, Y: 248.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 489.75, Y: 268.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 489.75, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 507.25, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 524.75, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 542.25, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 559.75, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 577.25, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 594.75, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 612.25, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 629.75, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 647.25, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 664.75, Y: 288.409777334456, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 5.5, Y: 308.40977733445595, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 158.5, Y: 308.40977733445595, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 191.0, Y: 156.05870447429047, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 266.47763763996943, Y: 21.825903140896287, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 263.5, Y: 216.05870447429047, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 348.5, Y: 308.409777334456, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 433.58083000536624, Y: 210.2060698287014, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 506.0, Y: 268.409777334456, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 643.5, Y: 308.409777334456, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '81', X: 661.0, Y: 308.409777334456, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'BCOR, -20.7 ± 0.7
 kcal/mol, AUC: 0.645', X: 268.75, Y: 321.209777334456, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 679.0, 321.209777334456)
Updated viewBox: -0.25 0.0 684.25 326.209777334456
Updated SVG: /disk1/www/rails/humanrnamap/public/result/aa090649-b7de-4c56-ad84-21d96f1e7805/final_image/BCOR_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/aa090649-b7de-4c56-ad84-21d96f1e7805/final_image/BCOR_fold_final_1.svg
