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/748511f6-9d4e-400e-840b-422a5f341adc/final_image/RUNX1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.39 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.39 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.39 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.01 MB
Based on canonical annotations, the following gene is in your area of interest: RUNX1(-)
write fasta - Elapsed time since the previous call: 0.13 seconds
write fasta - Current memory usage: 172.01 MB
Length of region: 122 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: 0.20 seconds
write dat - Current memory usage: 175.10 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/748511f6-9d4e-400e-840b-422a5f341adc/fasta/RUNX1.fasta" "/disk1/www/rails/humanrnamap/public/result/748511f6-9d4e-400e-840b-422a5f341adc/ct/RUNX1.ct" --SHAPE "RUNX1.dat"

fold - Elapsed time since the previous call: 0.18 seconds
fold - Current memory usage: 175.10 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/748511f6-9d4e-400e-840b-422a5f341adc/ct/RUNX1.ct" "/disk1/www/rails/humanrnamap/public/result/748511f6-9d4e-400e-840b-422a5f341adc/fold_FE/RUNX1.txt" -sh "RUNX1.dat"

efn2 - Elapsed time since the previous call: 0.52 seconds
efn2 - Current memory usage: 175.10 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/748511f6-9d4e-400e-840b-422a5f341adc/ct/RUNX1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/748511f6-9d4e-400e-840b-422a5f341adc/fold_dbn/RUNX1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.10 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CUUCCAGAAGAGUUGCAUCAACAAAGUUAAUUGUAUUUAUGUAUGUAAAUAGAUUUUAAGCUUCAUUAUAAAAUAUUGUUAAUGCCUAUAACUUUUUUUCAAUUUUUUUGUGUGUGUUUCUA', '-structureDBN', '....(((((((((((.......(((((((...(((((...((((((((..((........))...))))...))))....)))))...)))))))....)))))))))))............', '-o', '/disk1/www/rails/humanrnamap/public/result/748511f6-9d4e-400e-840b-422a5f341adc/final_image/RUNX1_fold_1.svg', '-title', 'RUNX1, -14.2 ± 1.5\n kcal/mol, AUC: 0.678', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,7,10,12,13,14,15,18,26,27,28,31,32,33,34,36,37,38,40,41,42,44,45,46,50,52,54,55,56,57,60,62,63,66,67,69,74,76,77,78,79,80,83,84,87,89,93,94,95,96,97,98,99,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,121', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '101,102,75,92,47', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,68,6,70,71,73,11,17,81,19,20,23,24,25,88,90,91,29,30,35,39,43,49,51,58', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,65,4,5,8,9,72,16,82,21,22,85,86,100,48,53,120,122,59,61']
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Text: 'A', X: 317.25, Y: 785.5667705863773, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 5.5, Y: 805.5667705863773, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 51.0, Y: 685.5667705863773, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 34.155225461201944, Y: 500.64473626278306, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 136.87847284620074, Y: 376.3335708660738, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 231.97869807876822, Y: 213.49359607993063, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 185.03482135279052, Y: 107.857191018712, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 203.11369896370675, Y: 13.069086816337972, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 326.79456140588707, Y: 115.29793588590894, 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: '110', X: 113.14213562373095, Y: 799.7089062101082, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '120', X: 274.0, Y: 805.5667705863773, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '122', X: 309.0, Y: 805.5667705863773, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'RUNX1, -14.2 ± 1.5
 kcal/mol, AUC: 0.678', X: 100.78083692527747, Y: 818.3667705863772, Width: 142.5, Height: 23
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Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/748511f6-9d4e-400e-840b-422a5f341adc/final_image/RUNX1_fold_final_1.svg
