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/1b354360-283e-420f-b092-8d694dbeb415/final_image/HTT_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.15 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.15 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.15 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 171.71 MB
Based on canonical annotations, the following gene is in your area of interest: HTT(+)
write fasta - Elapsed time since the previous call: 0.69 seconds
write fasta - Current memory usage: 171.71 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: 175.36 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/1b354360-283e-420f-b092-8d694dbeb415/fasta/HTT.fasta" "/disk1/www/rails/humanrnamap/public/result/1b354360-283e-420f-b092-8d694dbeb415/ct/HTT.ct" --SHAPE "HTT.dat"

fold - Elapsed time since the previous call: 0.13 seconds
fold - Current memory usage: 175.36 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/1b354360-283e-420f-b092-8d694dbeb415/ct/HTT.ct" "/disk1/www/rails/humanrnamap/public/result/1b354360-283e-420f-b092-8d694dbeb415/fold_FE/HTT.txt" -sh "HTT.dat"

efn2 - Elapsed time since the previous call: 0.42 seconds
efn2 - Current memory usage: 175.36 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/1b354360-283e-420f-b092-8d694dbeb415/ct/HTT.ct" 1 "/disk1/www/rails/humanrnamap/public/result/1b354360-283e-420f-b092-8d694dbeb415/fold_dbn/HTT_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.36 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'ACAAGCCUUGCCGCAUCAAAGGUGACAUUGGACAGUCCACUGAUGAUGACUCUGCACCUCUUGUCCAUUGUGUCCGCCUUUUAUCUGCUUCGUUUUUGCUAACA', '-structureDBN', '...(((...((.(((..((((((((((((((((((.....((..((....))..))....)))))))..))))).))))))....)))...))....)))....', '-o', '/disk1/www/rails/humanrnamap/public/result/1b354360-283e-420f-b092-8d694dbeb415/final_image/HTT_fold_1.svg', '-title', 'HTT, -25.9 ± 1.4\n kcal/mol, AUC: 0.753', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '5,8,9,10,13,16,21,22,23,24,28,29,30,31,35,36,41,42,44,45,47,48,51,53,54,59,61,62,63,64,68,69,70,71,72,73,76,79,80,81,82,84,86,87,89,90,92,93,94,95,96,97,98,100', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '65,66,3,6,78,77,14', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '67,4,7,74,11,75,15,17,18,19,83,85,88,25,26,27,32,33,37,38,39,101,102,46,49,50,52,55,56,58', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,2,34,99,103,40,104,43,12,20,57,91,60']
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Text: 'HTT, -25.9 ± 1.4
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Updated SVG: /disk1/www/rails/humanrnamap/public/result/1b354360-283e-420f-b092-8d694dbeb415/final_image/HTT_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/1b354360-283e-420f-b092-8d694dbeb415/final_image/HTT_fold_final_1.svg
