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/e4b4abcb-9e56-4af2-9b4d-25250d6454d8/final_image/KRAS_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 156.69 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 156.69 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 156.69 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 170.23 MB
Based on canonical annotations, the following gene is in your area of interest: KRAS(-)
write fasta - Elapsed time since the previous call: 0.53 seconds
write fasta - Current memory usage: 170.23 MB
Length of region: 105 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: 173.51 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/e4b4abcb-9e56-4af2-9b4d-25250d6454d8/fasta/KRAS.fasta" "/disk1/www/rails/humanrnamap/public/result/e4b4abcb-9e56-4af2-9b4d-25250d6454d8/ct/KRAS.ct" --SHAPE "KRAS.dat"

fold - Elapsed time since the previous call: 0.14 seconds
fold - Current memory usage: 173.51 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/e4b4abcb-9e56-4af2-9b4d-25250d6454d8/ct/KRAS.ct" "/disk1/www/rails/humanrnamap/public/result/e4b4abcb-9e56-4af2-9b4d-25250d6454d8/fold_FE/KRAS.txt" -sh "KRAS.dat"

efn2 - Elapsed time since the previous call: 0.43 seconds
efn2 - Current memory usage: 173.51 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/e4b4abcb-9e56-4af2-9b4d-25250d6454d8/ct/KRAS.ct" 1 "/disk1/www/rails/humanrnamap/public/result/e4b4abcb-9e56-4af2-9b4d-25250d6454d8/fold_dbn/KRAS_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 173.51 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AAGAGGUGAAGUUUAUAUUUGAAUAUCCAUUCUCGUUUUAGGACUCUUCUUCCAUAUUAGUGUCAUCUUGCCUCCCUACCUUCCACAUGCCCCAUGACUUGAUGC', '-structureDBN', '..(((((((.(((((....))))).).)).))))......(((.......))).((((((.(((((...((.................))...))))))))))).', '-o', '/disk1/www/rails/humanrnamap/public/result/e4b4abcb-9e56-4af2-9b4d-25250d6454d8/final_image/KRAS_fold_1.svg', '-title', 'KRAS, -10.6 ± 1.1\n kcal/mol, AUC: 0.352', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,5,6,7,8,11,12,13,14,16,18,19,20,21,24,26,30,31,33,35,36,37,38,39,41,42,45,47,48,50,51,55,57,58,60,61,62,63,66,68,69,70,73,77,81,82,88,89,95,96,99,100,101,103,104', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '64,65,67,4,40,72,74,75,76,80,52,53,85,91,92', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '2,71,105,10,78,79,49,83,84,86,90,59,28', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,9,15,17,22,23,87,25,27,29,93,94,32,97,34,98,102,43,44,46,54,56']
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Text: 'U', X: 208.98448533570016, Y: 391.71188070630296, Width: 10.5, Height: 8
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Text: 'U', X: 243.98448533570013, Y: 391.71188070630296, Width: 10.5, Height: 8
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Text: 'A', X: 261.4844853357001, Y: 391.71188070630296, Width: 10.5, Height: 8
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Text: 'G', X: 278.9844853357001, Y: 391.71188070630296, Width: 10.5, Height: 8
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Text: 'G', X: 278.9844853357001, Y: 371.71188070630296, Width: 10.5, Height: 8
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Text: 'A', X: 278.9844853357001, Y: 351.71188070630296, Width: 10.5, Height: 8
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Text: 'U', X: 342.66886646911746, Y: 274.63284904486795, Width: 10.5, Height: 8
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Text: 'G', X: 353.390207428257, Y: 260.80153971186564, Width: 10.5, Height: 8
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Text: 'U', X: 361.90182544350466, Y: 242.7031320812891, Width: 10.5, Height: 8
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Text: 'C', X: 370.41344345875245, Y: 224.60472445071267, Width: 10.5, Height: 8
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Text: 'C', X: 420.7379329096482, Y: 117.59891057950176, Width: 10.5, Height: 8
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Text: 'C', X: 409.78171223201343, Y: 103.95295658267696, Width: 10.5, Height: 8
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Text: 'C', X: 402.83561809417836, Y: 70.09431596191632, Width: 10.5, Height: 8
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Text: 'C', X: 512.7340592926583, Y: 66.29526774511635, Width: 10.5, Height: 8
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Text: 'U', X: 467.6458704665207, Y: 131.16630521611648, Width: 10.5, Height: 8
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Text: 'G', X: 450.14783811833274, Y: 131.43030514462748, Width: 10.5, Height: 8
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Text: 'C', X: 441.6362106936399, Y: 149.5287083499718, Width: 10.5, Height: 8
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Text: 'C', X: 447.74853364531987, Y: 165.926559066891, Width: 10.5, Height: 8
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Text: 'C', X: 433.3749775379624, Y: 196.48929126111878, Width: 10.5, Height: 8
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Text: 'A', X: 416.8465918889349, Y: 202.23928846433736, Width: 10.5, Height: 8
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Text: 'G', X: 399.8233558584393, Y: 238.4361037254903, Width: 10.5, Height: 8
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Text: 'A', X: 391.3117378431915, Y: 256.5345113560668, Width: 10.5, Height: 8
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Text: 'U', X: 378.9844853357001, Y: 291.71188070630296, Width: 10.5, Height: 8
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Text: 'U', X: 378.9844853357001, Y: 311.71188070630296, Width: 10.5, Height: 8
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Text: 'G', X: 378.9844853357001, Y: 331.71188070630296, Width: 10.5, Height: 8
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Text: 'A', X: 378.9844853357001, Y: 351.71188070630296, Width: 10.5, Height: 8
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Text: 'U', X: 378.9844853357001, Y: 371.711880706303, Width: 10.5, Height: 8
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Text: 'G', X: 378.9844853357001, Y: 391.711880706303, Width: 10.5, Height: 8
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Text: 'C', X: 396.4844853357001, Y: 391.711880706303, Width: 10.5, Height: 8
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Text: '1', X: 89.73448533570016, Y: 411.71188070630296, Width: 9.0, Height: 8
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Text: '10', X: 66.55219893174399, Y: 288.23047652277626, Width: 18.0, Height: 8
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Text: '20', X: 52.742255140109734, Y: 162.64803699920031, Width: 18.0, Height: 8
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Text: '30', X: 176.06894842168865, Y: 310.27226188845214, Width: 18.0, Height: 8
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Text: '40', X: 257.7344853357001, Y: 411.71188070630296, Width: 18.0, Height: 8
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Text: '50', X: 337.14440942630904, Y: 344.04787372748194, Width: 18.0, Height: 8
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Text: '80', X: 486.4893733811202, Y: 8.0, Width: 18.0, Height: 8
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Text: '90', X: 457.58373986892593, Y: 152.99386987416602, Width: 18.0, Height: 8
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Text: '100', X: 390.7344853357001, Y: 311.71188070630296, Width: 27.0, Height: 8
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Text: '105', X: 388.2344853357001, Y: 411.711880706303, Width: 27.0, Height: 8
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Text: 'KRAS, -10.6 ± 1.1
 kcal/mol, AUC: 0.352', X: 192.95918797981648, Y: 424.51188070630303, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 523.668375959633, 424.51188070630303)
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Updated SVG: /disk1/www/rails/humanrnamap/public/result/e4b4abcb-9e56-4af2-9b4d-25250d6454d8/final_image/KRAS_fold_final_1.svg
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