Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 95% [================================================  ] |                     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/18b4e363-9d52-4cd6-98c4-cd59cbef29e1/final_image/KRAS_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 157.06 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 157.06 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 157.06 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 170.66 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: 170.66 MB
Length of region: 100 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: 0.22 seconds
write dat - Current memory usage: 173.66 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/18b4e363-9d52-4cd6-98c4-cd59cbef29e1/fasta/KRAS.fasta" "/disk1/www/rails/humanrnamap/public/result/18b4e363-9d52-4cd6-98c4-cd59cbef29e1/ct/KRAS.ct" --SHAPE "KRAS.dat"

fold - Elapsed time since the previous call: 0.12 seconds
fold - Current memory usage: 173.66 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/18b4e363-9d52-4cd6-98c4-cd59cbef29e1/ct/KRAS.ct" "/disk1/www/rails/humanrnamap/public/result/18b4e363-9d52-4cd6-98c4-cd59cbef29e1/fold_FE/KRAS.txt" -sh "KRAS.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 173.66 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/18b4e363-9d52-4cd6-98c4-cd59cbef29e1/ct/KRAS.ct" 1 "/disk1/www/rails/humanrnamap/public/result/18b4e363-9d52-4cd6-98c4-cd59cbef29e1/fold_dbn/KRAS_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 173.66 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'ACUAUAAAGACUCCUAAUAGCUUUUCCUGUUAAGGCAGACCCAGUAUGAAAUGGGGAUUAUUAUAGCAACCAUUUUGGGGCUAUAUUUACAUGCUACUAA', '-structureDBN', '..........((((((((((......)))))).)).)).((((........))))......((((((..(((...))).))))))...............', '-o', '/disk1/www/rails/humanrnamap/public/result/18b4e363-9d52-4cd6-98c4-cd59cbef29e1/final_image/KRAS_fold_1.svg', '-title', 'KRAS, -22.8 ± 1.0\n kcal/mol, AUC: 0.729', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,5,9,12,15,18,20,22,23,24,25,28,29,30,31,34,35,38,44,45,47,48,52,53,54,55,56,58,59,61,62,64,66,73,74,75,76,77,78,79,80,82,84,86,87,88,92,93,95,98', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '65,67,68,99,70,71,100,43,49,81,85,63', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '32,69,41,42,11,13,17,83,57,60', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,2,4,6,7,8,72,10,14,16,19,21,89,26,27,90,91,94,96,33,97,36,37,39,40,46,50,51']
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Text: 'C', X: 402.25, Y: 112.8761102970536, Width: 10.5, Height: 8
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Text: 'A', X: 679.75, Y: 212.8761102970536, Width: 10.5, Height: 8
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Text: 'A', X: 697.25, Y: 212.8761102970536, Width: 10.5, Height: 8
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Text: '1', X: 5.5, Y: 232.87611029705357, Width: 9.0, Height: 8
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Text: '10', X: 158.5, Y: 232.87611029705357, Width: 18.0, Height: 8
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Text: '40', X: 229.35786437626905, Y: 227.01824592078452, Width: 18.0, Height: 8
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Text: '50', X: 310.1601866068412, Y: 119.86632918277019, Width: 18.0, Height: 8
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Text: '60', X: 363.5, Y: 232.87611029705357, Width: 18.0, Height: 8
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Text: '70', X: 388.1193087479924, Y: 60.83871819365089, Width: 18.0, Height: 8
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Text: '80', X: 450.9229876455946, Y: 114.62955355917683, Width: 18.0, Height: 8
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Text: '90', X: 518.5, Y: 232.87611029705357, Width: 18.0, Height: 8
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Text: '100', X: 689.0, Y: 232.8761102970536, Width: 27.0, Height: 8
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Text: 'KRAS, -22.8 ± 1.0
 kcal/mol, AUC: 0.729', X: 285.0, Y: 245.6761102970536, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 716.0, 245.6761102970536)
Updated viewBox: -0.25 0.0 721.25 250.6761102970536
Updated SVG: /disk1/www/rails/humanrnamap/public/result/18b4e363-9d52-4cd6-98c4-cd59cbef29e1/final_image/KRAS_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/18b4e363-9d52-4cd6-98c4-cd59cbef29e1/final_image/KRAS_fold_final_1.svg
