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/287a9f53-a8bb-46c4-8558-c2d8ca5f7eb5/final_image/HTT_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 157.94 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 157.94 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 157.94 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 171.51 MB
Based on canonical annotations, the following gene is in your area of interest: HTT(+)
write fasta - Elapsed time since the previous call: 0.67 seconds
write fasta - Current memory usage: 171.51 MB
Length of region: 92 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: 174.89 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/287a9f53-a8bb-46c4-8558-c2d8ca5f7eb5/fasta/HTT.fasta" "/disk1/www/rails/humanrnamap/public/result/287a9f53-a8bb-46c4-8558-c2d8ca5f7eb5/ct/HTT.ct" --SHAPE "HTT.dat"

fold - Elapsed time since the previous call: 0.10 seconds
fold - Current memory usage: 174.89 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/287a9f53-a8bb-46c4-8558-c2d8ca5f7eb5/ct/HTT.ct" "/disk1/www/rails/humanrnamap/public/result/287a9f53-a8bb-46c4-8558-c2d8ca5f7eb5/fold_FE/HTT.txt" -sh "HTT.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 174.89 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/287a9f53-a8bb-46c4-8558-c2d8ca5f7eb5/ct/HTT.ct" 1 "/disk1/www/rails/humanrnamap/public/result/287a9f53-a8bb-46c4-8558-c2d8ca5f7eb5/fold_dbn/HTT_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 174.89 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AACCUCACGAGUGUCACAAAGAACCGUGCAGAUAAGAAUGCUAUUCAUAAUCACAUUCGUUUGUUUGAACCUCUUGUUAUAAAAGCUUUAAA', '-structureDBN', '.....((((.((..........))))))((((((((((((.............)))))..))))))).........................', '-o', '/disk1/www/rails/humanrnamap/public/result/287a9f53-a8bb-46c4-8558-c2d8ca5f7eb5/final_image/HTT_fold_1.svg', '-title', 'HTT, -10.1 ± 0.6\n kcal/mol, AUC: 0.574', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '5,9,11,12,13,14,21,26,27,28,31,33,36,39,40,42,44,45,48,51,56,57,59,60,61,62,63,64,65,66,67,72,74,75,76,77,78,80,85,87,88,89', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '7,37,38,6,91', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '2,4,68,69,71,10,15,79,81,18,82,84,25,92,29,52,55,58', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,3,70,8,73,16,17,19,20,83,22,23,24,86,90,30,32,34,35,41,43,46,47,49,50,53,54']
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Text: '92', X: 608.5, Y: 320.9316415296101, Width: 18.0, Height: 8
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Text: 'HTT, -10.1 ± 0.6
 kcal/mol, AUC: 0.574', X: 242.5, Y: 333.7316415296101, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 626.5, 333.7316415296101)
Updated viewBox: -0.25 -5.0 631.75 343.7316415296101
Updated SVG: /disk1/www/rails/humanrnamap/public/result/287a9f53-a8bb-46c4-8558-c2d8ca5f7eb5/final_image/HTT_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/287a9f53-a8bb-46c4-8558-c2d8ca5f7eb5/final_image/HTT_fold_final_1.svg
