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/b262e985-b5dd-4d61-bad0-2d197140e745/final_image/KRAS_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 156.70 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 156.70 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 156.70 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 170.33 MB
Based on canonical annotations, the following gene is in your area of interest: KRAS(-)
write fasta - Elapsed time since the previous call: 0.54 seconds
write fasta - Current memory usage: 170.33 MB
Length of region: 133 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: 0.24 seconds
write dat - Current memory usage: 173.56 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/b262e985-b5dd-4d61-bad0-2d197140e745/fasta/KRAS.fasta" "/disk1/www/rails/humanrnamap/public/result/b262e985-b5dd-4d61-bad0-2d197140e745/ct/KRAS.ct" --SHAPE "KRAS.dat"

fold - Elapsed time since the previous call: 0.20 seconds
fold - Current memory usage: 173.56 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/b262e985-b5dd-4d61-bad0-2d197140e745/ct/KRAS.ct" "/disk1/www/rails/humanrnamap/public/result/b262e985-b5dd-4d61-bad0-2d197140e745/fold_FE/KRAS.txt" -sh "KRAS.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 173.56 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/b262e985-b5dd-4d61-bad0-2d197140e745/ct/KRAS.ct" 1 "/disk1/www/rails/humanrnamap/public/result/b262e985-b5dd-4d61-bad0-2d197140e745/fold_dbn/KRAS_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 173.56 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'ACUUUGUGGGGCAUGUUAAGUUACAGUUUGCACAAGUUCAUCUCAUUUGUAUUCCAUUGAUUUUUUUUUUCUUCUAAACAUUUUUUCUUCAAACAGUAUAUAACUUUUUUUAGGGGAUUUUUUUUUAGACAGC', '-structureDBN', '..((((((.(((.(((......)))).)).)))))).(((.................)))............((((((....((((((..(((.(((.....))).)))..))))))......))))))....', '-o', '/disk1/www/rails/humanrnamap/public/result/b262e985-b5dd-4d61-bad0-2d197140e745/final_image/KRAS_fold_1.svg', '-title', 'KRAS, -14.8 ± 1.7\n kcal/mol, AUC: 0.689', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,4,5,6,7,8,9,10,11,14,15,16,17,20,21,22,26,27,28,29,30,36,37,38,41,43,46,47,48,49,50,52,53,57,58,59,61,62,63,64,65,66,67,68,69,70,72,73,75,81,82,83,84,85,86,88,89,96,97,99,101,105,106,107,108,109,110,111,113,114,115,116,118,119,120,121,122,123,124,125,126,128,132', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '129,131,133,92,80,117,60,127', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '71,12,13,76,77,78,18,87,24,25,91,93,95,32,102,39,40,104,45,55,56', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,2,130,74,79,19,23,90,94,31,33,34,35,98,100,103,42,44,112,51,54']
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Text: 'U', X: 399.75, Y: 379.32283196067306, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 399.75, Y: 399.32283196067306, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 399.75, Y: 419.32283196067306, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 399.75, Y: 439.32283196067306, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 399.75, Y: 459.32283196067306, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 399.75, Y: 479.32283196067306, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 417.25, Y: 479.32283196067306, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 434.75, Y: 479.32283196067306, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 452.25, Y: 479.32283196067306, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 469.75, Y: 479.32283196067306, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 5.5, Y: 499.32283196067306, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 16.0, Y: 346.9717591005075, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 57.13925615989922, Y: 176.57248405781917, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 95.17837715148926, Y: 363.14729553059027, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 85.75111797240817, Y: 448.5411391138671, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 143.24925618102404, Y: 314.3114188842524, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 150.14213562373095, Y: 493.464967584404, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
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Warning: Font Verdana not found. Using default font.
Text: '80', X: 320.5387648530813, Y: 363.0876820578892, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
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Warning: Font Verdana not found. Using default font.
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Warning: Font Verdana not found. Using default font.
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Warning: Font Verdana not found. Using default font.
Text: '130', X: 409.0, Y: 499.32283196067306, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '133', X: 461.5, Y: 499.32283196067306, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'KRAS, -14.8 ± 1.7
 kcal/mol, AUC: 0.689', X: 171.25, Y: 512.122831960673, Width: 142.5, Height: 23
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Updated SVG: /disk1/www/rails/humanrnamap/public/result/b262e985-b5dd-4d61-bad0-2d197140e745/final_image/KRAS_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/b262e985-b5dd-4d61-bad0-2d197140e745/final_image/KRAS_fold_final_1.svg
