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/acefaa0e-f0dd-491a-af1c-0bc6d38228b4/final_image/KRAS_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 156.22 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 156.22 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 156.22 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 169.76 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: 169.76 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: 0.21 seconds
write dat - Current memory usage: 173.14 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/acefaa0e-f0dd-491a-af1c-0bc6d38228b4/fasta/KRAS.fasta" "/disk1/www/rails/humanrnamap/public/result/acefaa0e-f0dd-491a-af1c-0bc6d38228b4/ct/KRAS.ct" --SHAPE "KRAS.dat"

fold - Elapsed time since the previous call: 0.13 seconds
fold - Current memory usage: 173.14 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/acefaa0e-f0dd-491a-af1c-0bc6d38228b4/ct/KRAS.ct" "/disk1/www/rails/humanrnamap/public/result/acefaa0e-f0dd-491a-af1c-0bc6d38228b4/fold_FE/KRAS.txt" -sh "KRAS.dat"

efn2 - Elapsed time since the previous call: 0.42 seconds
efn2 - Current memory usage: 173.14 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/acefaa0e-f0dd-491a-af1c-0bc6d38228b4/ct/KRAS.ct" 1 "/disk1/www/rails/humanrnamap/public/result/acefaa0e-f0dd-491a-af1c-0bc6d38228b4/fold_dbn/KRAS_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 173.14 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CGACACAGCAGGUCAAGAGGAGUACAGUGCAAUGAGGGACCAGUACAUGAGGACUGGGGAGGGCUUUCUUUGUGUAUUUGCCAUAAAUAAUACUAAAUCAUUUGA', '-structureDBN', '..........((((.......(((...))).......)))).(((((((((((..((......)).)))))))))))............................', '-o', '/disk1/www/rails/humanrnamap/public/result/acefaa0e-f0dd-491a-af1c-0bc6d38228b4/final_image/KRAS_fold_1.svg', '-title', 'KRAS, -13.4 ± 0.8\n kcal/mol, AUC: 0.615', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,8,11,12,13,17,19,20,22,23,27,28,29,33,34,36,37,38,43,44,48,49,51,52,55,56,57,58,59,61,62,63,65,66,67,69,70,71,72,73,74,75,77,78,79,80,84,88,91,94,98,101,102,103,104', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '42,53,46,95', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '64,1,97,40,76,45,14,15,82,21,85,90', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '3,4,5,6,7,9,10,16,18,24,25,26,30,31,32,35,39,41,47,50,54,60,68,81,83,86,87,89,92,93,96,99,100,105']
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Text: '50', X: 223.5, Y: 188.69942936766452, Width: 18.0, Height: 8
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Text: 'KRAS, -13.4 ± 0.8
 kcal/mol, AUC: 0.615', X: 321.25, Y: 361.49942936766456, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 788.5, 361.49942936766456)
Updated viewBox: -0.25 -5.0 793.75 371.49942936766456
Updated SVG: /disk1/www/rails/humanrnamap/public/result/acefaa0e-f0dd-491a-af1c-0bc6d38228b4/final_image/KRAS_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/acefaa0e-f0dd-491a-af1c-0bc6d38228b4/final_image/KRAS_fold_final_1.svg
