Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 98% [==================================================] \                     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/ac6fa6fc-6a11-4d19-b2e9-4d7bca1d2294/final_image/KRAS_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 155.44 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 155.44 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 155.44 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 168.94 MB
Based on canonical annotations, the following gene is in your area of interest: KRAS(-)
write fasta - Elapsed time since the previous call: 0.56 seconds
write fasta - Current memory usage: 168.94 MB
Length of region: 91 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: 172.04 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/ac6fa6fc-6a11-4d19-b2e9-4d7bca1d2294/fasta/KRAS.fasta" "/disk1/www/rails/humanrnamap/public/result/ac6fa6fc-6a11-4d19-b2e9-4d7bca1d2294/ct/KRAS.ct" --SHAPE "KRAS.dat"

fold - Elapsed time since the previous call: 0.12 seconds
fold - Current memory usage: 172.04 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/ac6fa6fc-6a11-4d19-b2e9-4d7bca1d2294/ct/KRAS.ct" "/disk1/www/rails/humanrnamap/public/result/ac6fa6fc-6a11-4d19-b2e9-4d7bca1d2294/fold_FE/KRAS.txt" -sh "KRAS.dat"

efn2 - Elapsed time since the previous call: 0.50 seconds
efn2 - Current memory usage: 172.04 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/ac6fa6fc-6a11-4d19-b2e9-4d7bca1d2294/ct/KRAS.ct" 1 "/disk1/www/rails/humanrnamap/public/result/ac6fa6fc-6a11-4d19-b2e9-4d7bca1d2294/fold_dbn/KRAS_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 172.04 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CCCAAUCCAUUAGCGACAGUAGGAUUUUUCAAACCUGGUAUGAAUAGACAGAACCCUAUCCAGUGGAAGGAGAAUUUAAUAAAGAUAGUGC', '-structureDBN', '.......(((((.........(((((((((....((((.....((((........)))))))).....)))))))))........))))).', '-o', '/disk1/www/rails/humanrnamap/public/result/ac6fa6fc-6a11-4d19-b2e9-4d7bca1d2294/final_image/KRAS_fold_1.svg', '-title', 'KRAS, -11.7 ± 1.2\n kcal/mol, AUC: 0.62', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '6,10,11,13,15,19,20,22,23,25,26,27,28,29,36,37,38,39,41,42,45,47,51,57,59,63,64,65,66,69,70,72,75,76,77,80,84,86,88,89,90', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '1,2,3,14,87,24,56,61,31', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '67,68,5,7,71,9,74,12,16,82,21,30,33,35,48,58,62', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '4,8,73,78,79,17,18,81,83,85,91,32,34,40,43,44,46,49,50,52,53,54,55,60']
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Text: '1', X: 5.5, Y: 634.9599943438653, Width: 9.0, Height: 8
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Text: '10', X: 103.5, Y: 574.9599943438653, Width: 18.0, Height: 8
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Text: '30', X: 104.86635030502057, Y: 259.3529112062103, Width: 18.0, Height: 8
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Text: '40', X: 63.00456679195126, Y: 95.92829423144985, Width: 18.0, Height: 8
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Text: '50', X: 237.9745755992003, Y: 8.0, Width: 18.0, Height: 8
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Text: '60', X: 154.48245061518105, Y: 110.2821882869165, Width: 18.0, Height: 8
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Text: '70', X: 176.0, Y: 272.087438128372, Width: 18.0, Height: 8
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Text: '90', X: 170.14213562373095, Y: 629.1021299675963, Width: 18.0, Height: 8
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Text: '91', X: 173.5, Y: 634.9599943438653, Width: 18.0, Height: 8
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Text: 'KRAS, -11.7 ± 1.2
 kcal/mol, AUC: 0.62', X: 67.91621579037971, Y: 647.7599943438653, Width: 133.5, Height: 23
Calculated bounding box: (4.75, 0.0, 264.5824315807594, 647.7599943438653)
Updated viewBox: -0.25 -5.0 269.8324315807594 657.7599943438653
Updated SVG: /disk1/www/rails/humanrnamap/public/result/ac6fa6fc-6a11-4d19-b2e9-4d7bca1d2294/final_image/KRAS_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/ac6fa6fc-6a11-4d19-b2e9-4d7bca1d2294/final_image/KRAS_fold_final_1.svg
