Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 99% [==================================================] /                     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/99a2a2ee-eeaa-4127-bd4d-e1f5e7c0552a/final_image/HTT_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.98 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.98 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.98 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.54 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: 172.54 MB
Length of region: 101 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: 176.17 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/99a2a2ee-eeaa-4127-bd4d-e1f5e7c0552a/fasta/HTT.fasta" "/disk1/www/rails/humanrnamap/public/result/99a2a2ee-eeaa-4127-bd4d-e1f5e7c0552a/ct/HTT.ct" --SHAPE "HTT.dat"

fold - Elapsed time since the previous call: 0.12 seconds
fold - Current memory usage: 176.17 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/99a2a2ee-eeaa-4127-bd4d-e1f5e7c0552a/ct/HTT.ct" "/disk1/www/rails/humanrnamap/public/result/99a2a2ee-eeaa-4127-bd4d-e1f5e7c0552a/fold_FE/HTT.txt" -sh "HTT.dat"

efn2 - Elapsed time since the previous call: 0.42 seconds
efn2 - Current memory usage: 176.17 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/99a2a2ee-eeaa-4127-bd4d-e1f5e7c0552a/ct/HTT.ct" 1 "/disk1/www/rails/humanrnamap/public/result/99a2a2ee-eeaa-4127-bd4d-e1f5e7c0552a/fold_dbn/HTT_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 176.17 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AAACAGUUUGAAUACAUUGAAGUGGGCCAGUUCAGGGAAUCAGAGGCAAUCAUUCCAAACAUCUUUUUCUUCUUGGUAUUACUAUCUUAUGAACGCUAUCA', '-structureDBN', '...((.(((((.....))))).)).(((((...((((((..(((.................))).)))))).)))))........................', '-o', '/disk1/www/rails/humanrnamap/public/result/99a2a2ee-eeaa-4127-bd4d-e1f5e7c0552a/final_image/HTT_fold_1.svg', '-title', 'HTT, -12.0 ± 1.0\n kcal/mol, AUC: 0.61', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '6,7,8,9,10,13,17,18,19,22,23,24,25,26,30,31,32,35,36,37,40,43,45,46,50,53,54,62,64,65,66,67,68,70,71,73,74,75,76,77,79,80,83,85,87,88,90,91,95,97,99', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '59,12,92,48,93,56,89,27,28,29,63', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '2,3,69,39,72,14,51,20,21,84,55,57,58', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,4,5,11,78,15,16,81,82,86,94,96,33,34,98,100,101,38,41,42,44,47,49,52,60,61']
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Text: 'HTT, -12.0 ± 1.0
 kcal/mol, AUC: 0.61', X: 229.5, Y: 396.0609481568638, Width: 133.5, Height: 23
Calculated bounding box: (4.75, 0.0, 596.0, 396.0609481568638)
Updated viewBox: -0.25 -5.0 601.25 406.0609481568638
Updated SVG: /disk1/www/rails/humanrnamap/public/result/99a2a2ee-eeaa-4127-bd4d-e1f5e7c0552a/final_image/HTT_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/99a2a2ee-eeaa-4127-bd4d-e1f5e7c0552a/final_image/HTT_fold_final_1.svg
