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/cb11748a-ac37-4305-ade9-7d8a5b7920cf/final_image/HTT_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.43 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.43 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.43 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 173.09 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: 173.09 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: 0.18 seconds
write dat - Current memory usage: 176.29 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/cb11748a-ac37-4305-ade9-7d8a5b7920cf/fasta/HTT.fasta" "/disk1/www/rails/humanrnamap/public/result/cb11748a-ac37-4305-ade9-7d8a5b7920cf/ct/HTT.ct" --SHAPE "HTT.dat"

fold - Elapsed time since the previous call: 0.13 seconds
fold - Current memory usage: 176.29 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/cb11748a-ac37-4305-ade9-7d8a5b7920cf/ct/HTT.ct" "/disk1/www/rails/humanrnamap/public/result/cb11748a-ac37-4305-ade9-7d8a5b7920cf/fold_FE/HTT.txt" -sh "HTT.dat"

efn2 - Elapsed time since the previous call: 0.40 seconds
efn2 - Current memory usage: 176.29 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/cb11748a-ac37-4305-ade9-7d8a5b7920cf/ct/HTT.ct" 1 "/disk1/www/rails/humanrnamap/public/result/cb11748a-ac37-4305-ade9-7d8a5b7920cf/fold_dbn/HTT_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.29 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AUGAUCUGUUUGGGGAUGCUGCACUGUAUCAGUCCCUGCCCACUCUGGCCCGGGCCCUGGCACAGUACCUGGUGGUGGUCUCCAAACUGCCCAGUCAUUUGCACC', '-structureDBN', '.......((((((((((((((((((((.((((.(((.(((......)))..)))..)))).))))).....))))).))))))))))..................', '-o', '/disk1/www/rails/humanrnamap/public/result/cb11748a-ac37-4305-ade9-7d8a5b7920cf/final_image/HTT_fold_1.svg', '-title', 'HTT, -38.5 ± 1.6\n kcal/mol, AUC: 0.764', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,5,7,8,9,10,11,12,13,14,15,17,18,20,21,25,26,27,29,32,33,37,38,44,46,47,48,52,53,54,58,59,60,65,66,70,71,72,73,74,75,76,77,78,79,81,88,89,94,95,98,99,100,101', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '16,80,19,83,84,22,87,24,91,97,34,35,36,40,104,105,50,57', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '68,41,49,82,51,85,86,56,62,90,92,61,30', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,1,67,4,69,6,23,28,93,31,96,102,39,103,42,43,45,55,63']
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Text: 'HTT, -38.5 ± 1.6
 kcal/mol, AUC: 0.764', X: 290.57139841839347, Y: 375.95961878305707, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 727.1427968367869, 375.95961878305707)
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Updated SVG: /disk1/www/rails/humanrnamap/public/result/cb11748a-ac37-4305-ade9-7d8a5b7920cf/final_image/HTT_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/cb11748a-ac37-4305-ade9-7d8a5b7920cf/final_image/HTT_fold_final_1.svg
