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/0fd9efdd-4753-4429-af8d-0f5ac99fd4a2/final_image/HTT_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.46 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.46 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.46 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 173.11 MB
Based on canonical annotations, the following gene is in your area of interest: HTT(+)
write fasta - Elapsed time since the previous call: 0.64 seconds
write fasta - Current memory usage: 173.11 MB
Length of region: 87 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: 0.17 seconds
write dat - Current memory usage: 176.36 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/0fd9efdd-4753-4429-af8d-0f5ac99fd4a2/fasta/HTT.fasta" "/disk1/www/rails/humanrnamap/public/result/0fd9efdd-4753-4429-af8d-0f5ac99fd4a2/ct/HTT.ct" --SHAPE "HTT.dat"

fold - Elapsed time since the previous call: 0.11 seconds
fold - Current memory usage: 176.36 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/0fd9efdd-4753-4429-af8d-0f5ac99fd4a2/ct/HTT.ct" "/disk1/www/rails/humanrnamap/public/result/0fd9efdd-4753-4429-af8d-0f5ac99fd4a2/fold_FE/HTT.txt" -sh "HTT.dat"

efn2 - Elapsed time since the previous call: 0.50 seconds
efn2 - Current memory usage: 176.36 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/0fd9efdd-4753-4429-af8d-0f5ac99fd4a2/ct/HTT.ct" 1 "/disk1/www/rails/humanrnamap/public/result/0fd9efdd-4753-4429-af8d-0f5ac99fd4a2/fold_dbn/HTT_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 176.36 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CUCGACAGAUAGCUGACAUCAUCCUCCCAAUGUUAGCCAAACAGCAGAUGCACAUUGACUCUCAUGAAGCCCUUGGAGUGUUAAAUA', '-structureDBN', '...........((((((((..........))))))))......((....))...(((((.(((............))).)))))...', '-o', '/disk1/www/rails/humanrnamap/public/result/0fd9efdd-4753-4429-af8d-0f5ac99fd4a2/final_image/HTT_fold_1.svg', '-title', 'HTT, -12.8 ± 0.8\n kcal/mol, AUC: 0.596', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,4,8,10,12,14,15,19,22,25,31,32,33,34,36,44,47,49,50,55,56,57,60,62,65,66,69,73,74,75,76,78,79,80,81,82,86', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '1,35,37,39,59,45,54,24,26,27,63', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '67,38,70,71,41,77,46,48,17,83,20,23,28', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,3,68,5,6,7,72,9,11,13,16,18,84,21,85,87,29,30,40,42,43,51,52,53,58,61']
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Text: 'HTT, -12.8 ± 0.8
 kcal/mol, AUC: 0.596', X: 206.25, Y: 292.0731959406177, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 554.0, 292.0731959406177)
Updated viewBox: -0.25 -5.0 559.25 302.0731959406177
Updated SVG: /disk1/www/rails/humanrnamap/public/result/0fd9efdd-4753-4429-af8d-0f5ac99fd4a2/final_image/HTT_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/0fd9efdd-4753-4429-af8d-0f5ac99fd4a2/final_image/HTT_fold_final_1.svg
