Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 97% [================================================= ] |                     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/3710bef2-fbc3-4f9d-9b84-e1a297e64ccc/final_image/KRAS_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 157.70 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 157.70 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 157.70 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 171.36 MB
Based on canonical annotations, the following gene is in your area of interest: KRAS(-)
write fasta - Elapsed time since the previous call: 1.12 seconds
write fasta - Current memory usage: 171.36 MB
Length of region: 97 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: 174.61 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/3710bef2-fbc3-4f9d-9b84-e1a297e64ccc/fasta/KRAS.fasta" "/disk1/www/rails/humanrnamap/public/result/3710bef2-fbc3-4f9d-9b84-e1a297e64ccc/ct/KRAS.ct" --SHAPE "KRAS.dat"

fold - Elapsed time since the previous call: 0.12 seconds
fold - Current memory usage: 174.61 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/3710bef2-fbc3-4f9d-9b84-e1a297e64ccc/ct/KRAS.ct" "/disk1/www/rails/humanrnamap/public/result/3710bef2-fbc3-4f9d-9b84-e1a297e64ccc/fold_FE/KRAS.txt" -sh "KRAS.dat"

efn2 - Elapsed time since the previous call: 0.40 seconds
efn2 - Current memory usage: 174.61 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/3710bef2-fbc3-4f9d-9b84-e1a297e64ccc/ct/KRAS.ct" 1 "/disk1/www/rails/humanrnamap/public/result/3710bef2-fbc3-4f9d-9b84-e1a297e64ccc/fold_dbn/KRAS_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 174.61 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AGAUAUUCACCAUUAUAGAGAACAAAUUAAAAGAGUUAAGGACUCUGAAGAUGUACCUAUGGUCCUAGUAGGAAAUAAAUGUGAUUUGCCUUCUAGA', '-structureDBN', '...........(((((((...(((.......((((((...)))))).....)))..))))))).((((.(((((((.......)))).))).)))).', '-o', '/disk1/www/rails/humanrnamap/public/result/3710bef2-fbc3-4f9d-9b84-e1a297e64ccc/final_image/KRAS_fold_1.svg', '-title', 'KRAS, -19.6 ± 0.9\n kcal/mol, AUC: 0.731', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,4,6,7,13,14,16,18,20,27,28,33,35,36,37,40,41,44,46,47,50,52,53,54,58,60,61,62,63,66,68,69,71,72,76,80,81,82,83,85,86,87,88,91,92,94,96', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '64,65,97,70,43,12,45,77,24,57,90,93,95', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,67,73,74,15,19,84,21,22,25,26,29,30,32,34,42,55', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '3,5,8,9,10,11,75,78,79,17,23,89,31,38,39,48,49,51,56,59']
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Text: 'G', X: 229.75, Y: 354.4726400507297, Width: 10.5, Height: 8
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Text: 'G', X: 229.75, Y: 374.4726400507297, Width: 10.5, Height: 8
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Text: 'U', X: 229.75, Y: 394.47264005072964, Width: 10.5, Height: 8
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Text: 'C', X: 264.75, Y: 394.4726400507297, Width: 10.5, Height: 8
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Text: 'U', X: 264.75, Y: 374.4726400507297, Width: 10.5, Height: 8
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Text: 'A', X: 264.75, Y: 354.4726400507297, Width: 10.5, Height: 8
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Text: 'U', X: 258.07162284851074, Y: 318.2971036206469, Width: 10.5, Height: 8
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Text: 'A', X: 264.75, Y: 302.1215671905642, Width: 10.5, Height: 8
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Text: 'G', X: 264.75, Y: 282.1215671905642, Width: 10.5, Height: 8
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Text: 'G', X: 264.75, Y: 262.1215671905642, Width: 10.5, Height: 8
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Text: 'A', X: 260.93439675932206, Y: 245.0424655874083, Width: 10.5, Height: 8
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Text: 'U', X: 235.39992122261452, Y: 190.74706468580996, Width: 10.5, Height: 8
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Text: 'A', X: 219.96830399281666, Y: 182.4938603322579, Width: 10.5, Height: 8
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Text: '1', X: 5.5, Y: 414.47264005072964, Width: 9.0, Height: 8
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Text: '10', X: 158.5, Y: 414.47264005072964, Width: 18.0, Height: 8
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Text: '30', X: 222.01916433078804, Y: 73.31643482631148, Width: 18.0, Height: 8
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Text: '40', X: 388.6129605789881, Y: 39.132263772389194, Width: 18.0, Height: 8
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Text: '50', X: 287.10128450464305, Y: 193.31044609518008, Width: 18.0, Height: 8
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Text: '60', X: 246.0, Y: 334.4726400507297, Width: 18.0, Height: 8
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Text: '70', X: 241.0, Y: 302.1215671905642, Width: 18.0, Height: 8
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Text: '80', X: 216.06233432908866, Y: 119.41862573454978, Width: 18.0, Height: 8
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Text: '90', X: 313.5, Y: 282.1215671905642, Width: 18.0, Height: 8
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Text: '97', X: 311.0, Y: 414.4726400507297, Width: 18.0, Height: 8
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Text: 'KRAS, -19.6 ± 0.9
 kcal/mol, AUC: 0.731', X: 122.81069672178543, Y: 427.2726400507297, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 406.6129605789881, 427.2726400507297)
Updated viewBox: -0.25 0.0 411.8629605789881 432.2726400507297
Updated SVG: /disk1/www/rails/humanrnamap/public/result/3710bef2-fbc3-4f9d-9b84-e1a297e64ccc/final_image/KRAS_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/3710bef2-fbc3-4f9d-9b84-e1a297e64ccc/final_image/KRAS_fold_final_1.svg
