Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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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/d47aec06-f868-4d46-972d-61a0bf4be215/final_image/SON_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.82 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.82 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.82 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.45 MB
Based on canonical annotations, the following gene is in your area of interest: SON(+)
write fasta - Elapsed time since the previous call: 0.13 seconds
write fasta - Current memory usage: 172.45 MB
Length of region: 141 nt.
98.5% 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: 0.21 seconds
write dat - Current memory usage: 176.25 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/d47aec06-f868-4d46-972d-61a0bf4be215/fasta/SON.fasta" "/disk1/www/rails/humanrnamap/public/result/d47aec06-f868-4d46-972d-61a0bf4be215/ct/SON.ct" --SHAPE "SON.dat"

fold - Elapsed time since the previous call: 0.25 seconds
fold - Current memory usage: 176.25 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/d47aec06-f868-4d46-972d-61a0bf4be215/ct/SON.ct" "/disk1/www/rails/humanrnamap/public/result/d47aec06-f868-4d46-972d-61a0bf4be215/fold_FE/SON.txt" -sh "SON.dat"

efn2 - Elapsed time since the previous call: 0.42 seconds
efn2 - Current memory usage: 176.25 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/d47aec06-f868-4d46-972d-61a0bf4be215/ct/SON.ct" 1 "/disk1/www/rails/humanrnamap/public/result/d47aec06-f868-4d46-972d-61a0bf4be215/fold_dbn/SON_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 176.25 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AUUAAAAUGCUGUAACCAACUUAUCUAAUAAAAUUGGCAACCAGCCACUAUUUUGUUGACUAUGAGAAAGUUAAAAGUUUAUGUUAAUUUUUAGGGUCUGAUAGAAUAUUUCAUGUGUAUUACAGUGGUAUUCAUAUGCUA', '-structureDBN', '........(((((((..........(((((((((((((.....))))..))))))))).((((.(((...(((((((((......)))))))))..))).)))).((((.....)))).))))))).((((....))))..', '-o', '/disk1/www/rails/humanrnamap/public/result/d47aec06-f868-4d46-972d-61a0bf4be215/final_image/SON_fold_1.svg', '-title', 'SON, -25.5 ± 1.4\n kcal/mol, AUC: 0.586', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,8,9,11,12,13,21,22,24,26,29,34,35,36,37,44,49,51,52,53,54,55,56,57,58,61,63,64,66,70,71,72,77,78,79,80,82,83,84,85,88,89,90,91,92,94,95,96,97,99,100,102,104,107,109,110,111,114,115,116,117,118,120,121,125,126,127,128,129,131,132,135,137,138,139,140', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '5,38,136,108,45,46,18,119,87,23,93,31', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '130,4,68,6,7,134,69,73,74,75,14,19,86,32,103,106,43,47,113,50,122', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,65,67,133,10,76,141,15,16,17,81,20,25,27,28,30,33,98,101,39,40,41,42,105,123,48,112,124,59,60,62']
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Text: 'A', X: 193.57638717740258, Y: 410.1775429113766, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 177.25, Y: 416.4782636426537, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 177.25, Y: 436.4782636426537, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 177.25, Y: 456.4782636426537, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 177.25, Y: 476.4782636426537, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 177.25, Y: 496.4782636426537, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 177.25, Y: 516.4782636426537, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 177.25, Y: 536.4782636426537, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 194.75, Y: 536.4782636426537, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 212.25, Y: 536.4782636426537, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 212.25, Y: 516.4782636426537, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 212.25, Y: 496.4782636426537, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 212.25, Y: 476.4782636426537, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 208.7012656127609, Y: 459.34181897506255, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 219.74998212006702, Y: 445.7706320285288, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 237.250017879933, Y: 445.7706320285288, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 248.2987343872391, Y: 459.34181897506255, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 244.75, Y: 476.4782636426537, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 244.75, Y: 496.4782636426537, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 244.75, Y: 516.4782636426537, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 244.75, Y: 536.4782636426537, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 262.25, Y: 536.4782636426537, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 279.75, Y: 536.4782636426537, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 5.5, Y: 556.4782636426537, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 121.0, Y: 516.4782636426537, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 68.98067032186484, Y: 354.2624551604612, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 145.04663220481658, Y: 199.7325285971785, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 100.25607683781973, Y: 28.540297443678583, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 229.48162271294444, Y: 132.44965424081022, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 213.8576778134341, Y: 288.5264317842984, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 382.7150161531383, Y: 212.65013759679175, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 560.4117842272848, Y: 214.50432797048836, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '90', X: 468.89079316999585, Y: 295.5285613895029, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '100', X: 300.52601054652905, Y: 331.7475898597298, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '110', X: 295.6823351275191, Y: 392.00270002392193, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '120', X: 186.18417640376003, Y: 426.71076486788974, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '130', X: 184.0, Y: 496.4782636426537, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '140', X: 254.0, Y: 556.4782636426537, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '141', X: 271.5, Y: 556.4782636426537, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'SON, -25.5 ± 1.4
 kcal/mol, AUC: 0.586', X: 234.5070764171254, Y: 569.2782636426537, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 606.7641528342508, 569.2782636426537)
Updated viewBox: -0.25 0.0 612.0141528342508 574.2782636426537
Updated SVG: /disk1/www/rails/humanrnamap/public/result/d47aec06-f868-4d46-972d-61a0bf4be215/final_image/SON_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/d47aec06-f868-4d46-972d-61a0bf4be215/final_image/SON_fold_final_1.svg
