Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  6% [====                                              ] -                     
 12% [=======                                           ] \                     
 18% [==========                                        ] |                     
 24% [=============                                     ] /                     
 30% [================                                  ] -                     
 36% [===================                               ] \                     
 42% [======================                            ] |                     
 48% [=========================                         ] /                     
 54% [============================                      ] -                     
 60% [===============================                   ] \                     
 66% [==================================                ] |                     
 72% [=====================================             ] /                     
 78% [========================================          ] -                     
 84% [===========================================       ] \                     
 90% [==============================================    ] |                     
 96% [================================================= ] /                     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/96d65170-87f0-46f4-b1e6-8d66d572c932/final_image/BCOR_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 157.94 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 157.94 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 157.94 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 171.51 MB
Based on canonical annotations, the following gene is in your area of interest: BCOR(-)
write fasta - Elapsed time since the previous call: 0.26 seconds
write fasta - Current memory usage: 171.51 MB
Length of region: 83 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: 174.91 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/96d65170-87f0-46f4-b1e6-8d66d572c932/fasta/BCOR.fasta" "/disk1/www/rails/humanrnamap/public/result/96d65170-87f0-46f4-b1e6-8d66d572c932/ct/BCOR.ct" --SHAPE "BCOR.dat"

fold - Elapsed time since the previous call: 0.09 seconds
fold - Current memory usage: 174.91 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/96d65170-87f0-46f4-b1e6-8d66d572c932/ct/BCOR.ct" "/disk1/www/rails/humanrnamap/public/result/96d65170-87f0-46f4-b1e6-8d66d572c932/fold_FE/BCOR.txt" -sh "BCOR.dat"

efn2 - Elapsed time since the previous call: 0.50 seconds
efn2 - Current memory usage: 174.91 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/96d65170-87f0-46f4-b1e6-8d66d572c932/ct/BCOR.ct" 1 "/disk1/www/rails/humanrnamap/public/result/96d65170-87f0-46f4-b1e6-8d66d572c932/fold_dbn/BCOR_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 174.91 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CAUAGAGAUUACUAAAGAGGAGAAACCAGAGAGGAGAUCCCGGUCCCAUGAGAGAGCCCGUUACGAGGACCCAACCCUCCGGA', '-structureDBN', '..................((.....)).....((((.....(((((..(((.........)))...))))).....))))...', '-o', '/disk1/www/rails/humanrnamap/public/result/96d65170-87f0-46f4-b1e6-8d66d572c932/final_image/BCOR_fold_1.svg', '-title', 'BCOR, -16.6 ± 0.7\n kcal/mol, AUC: 0.844', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,5,7,9,10,13,17,19,20,22,29,31,33,34,36,38,42,43,44,49,50,52,54,56,60,61,62,65,67,68,78,81,82', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '1,69,70,71,76,45,46,77,79,51,23,58,27,28', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '2,35,39,73,11,14,47,80,18,21,24,57,63', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,66,4,6,8,72,74,75,12,15,16,83,25,26,30,32,37,40,41,48,53,55,59']
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 4.75, Y: 385.3700428192568, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 22.25, Y: 385.3700428192568, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 39.75, Y: 385.3700428192568, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 57.25, Y: 385.3700428192568, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 74.75, Y: 385.3700428192568, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 92.25, Y: 385.3700428192568, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 109.75, Y: 385.3700428192568, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 127.25, Y: 385.3700428192568, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 144.75, Y: 385.3700428192568, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 162.25, Y: 385.3700428192568, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 179.75, Y: 385.3700428192568, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 197.25, Y: 385.3700428192568, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 214.75, Y: 385.3700428192568, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 232.25, Y: 385.3700428192568, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 249.75, Y: 385.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 267.25, Y: 385.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 284.75, Y: 385.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 302.25, Y: 385.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 319.75, Y: 385.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 319.75, Y: 365.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 313.1018303951821, Y: 349.1820025196023, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 319.82804965122153, Y: 333.0262362933488, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 336.0, Y: 326.3390223926044, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 352.17195034877847, Y: 333.0262362933488, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 358.8981696048179, Y: 349.1820025196023, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 352.25, Y: 365.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 352.25, Y: 385.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 369.75, Y: 385.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 387.25, Y: 385.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 404.75, Y: 385.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 422.25, Y: 385.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 439.75, Y: 385.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 457.25, Y: 385.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 457.25, Y: 365.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 457.25, Y: 345.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 457.25, Y: 325.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 442.5665000621637, Y: 315.8492313656187, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 432.7238804490855, Y: 301.3794746187893, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 429.26244354248047, Y: 284.22519014808756, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 432.7238804490855, Y: 267.07090567738584, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 442.5665000621637, Y: 252.6011489305564, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 457.25, Y: 243.08033747691826, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 457.25, Y: 223.08033747691826, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 457.25, Y: 203.08033747691826, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 457.25, Y: 183.08033747691826, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 457.25, Y: 163.08033747691826, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 445.6688475784504, Y: 149.96067940589245, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 443.1464749042966, Y: 132.64345805243966, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 450.503890685691, Y: 116.76526696115081, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 444.7986567753516, Y: 97.59627361177752, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 439.09342286501226, Y: 78.42728026240434, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 423.56734216565957, Y: 70.35322959316682, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 414.21279866263933, Y: 55.56330085965601, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 413.57089970799035, Y: 38.07509220856059, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 421.81601342052, Y: 22.639173837446947, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 436.70840260016723, Y: 13.448623222051083, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 454.2026363157909, Y: 13.0, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 469.54650769607736, Y: 21.415170061113145, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 478.5719432951558, Y: 36.40820138700303, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 478.8272360095458, Y: 53.90632419267013, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 470.24303705774366, Y: 69.15627515810297, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 475.948270968083, Y: 88.32526850747615, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 481.65350487842244, Y: 107.49426185684933, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 496.4960216824268, Y: 116.76516768761087, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 503.8535123716812, Y: 132.64337069543058, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 501.3311709789348, Y: 149.96063935704228, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 489.75, Y: 163.08033747691826, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 489.75, Y: 183.08033747691826, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 489.75, Y: 203.08033747691826, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 489.75, Y: 223.08033747691826, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 489.75, Y: 243.08033747691826, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 504.43349993783636, Y: 252.6011489305564, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 514.2761195509145, Y: 267.0709056773858, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 517.7375564575195, Y: 284.22519014808756, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 514.2761195509145, Y: 301.3794746187893, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 504.43349993783636, Y: 315.8492313656187, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 489.75, Y: 325.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 489.75, Y: 345.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 489.75, Y: 365.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 489.75, Y: 385.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 507.25, Y: 385.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 524.75, Y: 385.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 542.25, Y: 385.37004281925687, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 5.5, Y: 405.3700428192568, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 158.5, Y: 405.3700428192568, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 301.8408113363105, Y: 379.495104815087, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 401.0, Y: 405.37004281925687, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 410.5388117806472, Y: 259.31537583152976, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 421.8796634259784, Y: 103.30150752211682, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 494.46016489203396, Y: 58.836036956757596, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 506.0, Y: 223.08033747691826, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 500.14213562373095, Y: 399.5121784429878, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '83', X: 538.5, Y: 405.37004281925687, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'BCOR, -16.6 ± 0.7
 kcal/mol, AUC: 0.844', X: 207.5, Y: 418.1700428192569, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 556.5, 418.1700428192569)
Updated viewBox: -0.25 0.0 561.75 423.1700428192569
Updated SVG: /disk1/www/rails/humanrnamap/public/result/96d65170-87f0-46f4-b1e6-8d66d572c932/final_image/BCOR_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/96d65170-87f0-46f4-b1e6-8d66d572c932/final_image/BCOR_fold_final_1.svg
