Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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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/62b8a5f0-ab37-42ae-973f-8179f94caf35/final_image/HTT_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 155.12 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 155.12 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 155.12 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 168.66 MB
Based on canonical annotations, the following gene is in your area of interest: HTT(+)
write fasta - Elapsed time since the previous call: 0.68 seconds
write fasta - Current memory usage: 168.66 MB
Length of region: 104 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: 0.18 seconds
write dat - Current memory usage: 171.58 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/62b8a5f0-ab37-42ae-973f-8179f94caf35/fasta/HTT.fasta" "/disk1/www/rails/humanrnamap/public/result/62b8a5f0-ab37-42ae-973f-8179f94caf35/ct/HTT.ct" --SHAPE "HTT.dat"

fold - Elapsed time since the previous call: 0.13 seconds
fold - Current memory usage: 171.58 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/62b8a5f0-ab37-42ae-973f-8179f94caf35/ct/HTT.ct" "/disk1/www/rails/humanrnamap/public/result/62b8a5f0-ab37-42ae-973f-8179f94caf35/fold_FE/HTT.txt" -sh "HTT.dat"

efn2 - Elapsed time since the previous call: 0.40 seconds
efn2 - Current memory usage: 171.58 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/62b8a5f0-ab37-42ae-973f-8179f94caf35/ct/HTT.ct" 1 "/disk1/www/rails/humanrnamap/public/result/62b8a5f0-ab37-42ae-973f-8179f94caf35/fold_dbn/HTT_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 171.58 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CCUCUGAAAGCUCUCGACACCAGGUUUGGGAGGAAGCUGAGCAUUAUCAGAGGGAUUGUGGAGCAAGAGAUUCAAGCAAUGGUUUCAAAGAGAGAGAAUAUUGC', '-structureDBN', '(((((((..((((((....(((....)))...))....))))....))))))).....((((........)))).((((((.((((.......)))).))))))', '-o', '/disk1/www/rails/humanrnamap/public/result/62b8a5f0-ab37-42ae-973f-8179f94caf35/final_image/HTT_fold_1.svg', '-title', 'HTT, -29.1 ± 1.7\n kcal/mol, AUC: 0.736', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,5,6,10,12,14,16,23,24,25,26,27,28,29,30,32,33,36,38,39,41,44,45,47,50,52,53,54,56,57,58,59,60,61,63,67,69,71,72,76,80,81,82,83,84,85,90,92,94,96,99,101,102,103', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '64,2,4,104,11,13,18,51,21,91,62,95', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '97,34,37,40,73,42,75,15,48,49,20,22,87,88,93', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,65,66,68,70,7,8,9,74,77,78,79,17,19,86,89,31,98,35,100,43,46,55']
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Text: 'HTT, -29.1 ± 1.7
 kcal/mol, AUC: 0.736', X: 170.9878284552981, Y: 319.3979978294364, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 4.055303862805658, 497.37653663379933, 319.3979978294364)
Updated viewBox: -0.25 -0.9446961371943416 502.62653663379933 325.34269396663075
Updated SVG: /disk1/www/rails/humanrnamap/public/result/62b8a5f0-ab37-42ae-973f-8179f94caf35/final_image/HTT_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/62b8a5f0-ab37-42ae-973f-8179f94caf35/final_image/HTT_fold_final_1.svg
