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/bbb2bb5f-7e43-4f2d-8420-c66ffb1d8ff6/final_image/KRAS_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 155.43 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 155.43 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 155.43 MB
read annotations - Elapsed time since the previous call: 0.10 seconds
read annotations - Current memory usage: 168.88 MB
Based on canonical annotations, the following gene is in your area of interest: KRAS(-)
write fasta - Elapsed time since the previous call: 0.54 seconds
write fasta - Current memory usage: 168.88 MB
Length of region: 107 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: 172.07 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/bbb2bb5f-7e43-4f2d-8420-c66ffb1d8ff6/fasta/KRAS.fasta" "/disk1/www/rails/humanrnamap/public/result/bbb2bb5f-7e43-4f2d-8420-c66ffb1d8ff6/ct/KRAS.ct" --SHAPE "KRAS.dat"

fold - Elapsed time since the previous call: 0.13 seconds
fold - Current memory usage: 172.07 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/bbb2bb5f-7e43-4f2d-8420-c66ffb1d8ff6/ct/KRAS.ct" "/disk1/www/rails/humanrnamap/public/result/bbb2bb5f-7e43-4f2d-8420-c66ffb1d8ff6/fold_FE/KRAS.txt" -sh "KRAS.dat"

efn2 - Elapsed time since the previous call: 0.50 seconds
efn2 - Current memory usage: 172.07 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/bbb2bb5f-7e43-4f2d-8420-c66ffb1d8ff6/ct/KRAS.ct" 1 "/disk1/www/rails/humanrnamap/public/result/bbb2bb5f-7e43-4f2d-8420-c66ffb1d8ff6/fold_dbn/KRAS_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 172.07 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AGGACUCUGAUUUUGAGGACAUCACUUACUAUCCAUUUCUUCAUGUUAAAAGAAGUCAUCUCAAACUCUUAGUUUUUUUUUUUUACAACUAUGUAAUUUAUAUUCCA', '-structureDBN', '((((((..((.(((((((((.((..((((...............).)))..)).)))..)))))).))..))))))......(((((....)))))...........', '-o', '/disk1/www/rails/humanrnamap/public/result/bbb2bb5f-7e43-4f2d-8420-c66ffb1d8ff6/final_image/KRAS_fold_1.svg', '-title', 'KRAS, -14.4 ± 1.4\n kcal/mol, AUC: 0.731', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,6,8,9,11,12,13,14,15,17,18,22,26,27,30,32,36,37,38,40,41,44,45,46,47,52,55,56,59,61,67,69,70,72,73,74,75,76,77,78,79,80,81,82,83,84,90,92,93,94,97,98,99,101,103,104', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '16,48,100,85,71,95', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,4,5,19,20,23,28,96,39,105,106,43,107,54,57,58,60,62,63', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,65,66,68,7,10,21,86,87,24,25,88,89,91,29,31,33,34,35,102,42,49,50,51,53']
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Text: 'KRAS, -14.4 ± 1.4
 kcal/mol, AUC: 0.731', X: 246.96988649149057, Y: 590.596555715655, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 639.9397729829811, 590.596555715655)
Updated viewBox: -0.25 -5.0 645.1897729829811 600.596555715655
Updated SVG: /disk1/www/rails/humanrnamap/public/result/bbb2bb5f-7e43-4f2d-8420-c66ffb1d8ff6/final_image/KRAS_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/bbb2bb5f-7e43-4f2d-8420-c66ffb1d8ff6/final_image/KRAS_fold_final_1.svg
