Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 95% [================================================  ] -                     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/3553bd62-7f88-4b7e-ad7c-880b43a0fdf5/final_image/ITCH_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 157.92 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 157.92 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 157.92 MB
read annotations - Elapsed time since the previous call: 0.10 seconds
read annotations - Current memory usage: 172.45 MB
Based on canonical annotations, the following gene is in your area of interest: ITCH(+)
write fasta - Elapsed time since the previous call: 0.58 seconds
write fasta - Current memory usage: 172.45 MB
Length of region: 89 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: 176.02 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/3553bd62-7f88-4b7e-ad7c-880b43a0fdf5/fasta/ITCH.fasta" "/disk1/www/rails/humanrnamap/public/result/3553bd62-7f88-4b7e-ad7c-880b43a0fdf5/ct/ITCH.ct" --SHAPE "ITCH.dat"

fold - Elapsed time since the previous call: 0.10 seconds
fold - Current memory usage: 176.02 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/3553bd62-7f88-4b7e-ad7c-880b43a0fdf5/ct/ITCH.ct" "/disk1/www/rails/humanrnamap/public/result/3553bd62-7f88-4b7e-ad7c-880b43a0fdf5/fold_FE/ITCH.txt" -sh "ITCH.dat"

efn2 - Elapsed time since the previous call: 0.53 seconds
efn2 - Current memory usage: 176.02 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/3553bd62-7f88-4b7e-ad7c-880b43a0fdf5/ct/ITCH.ct" 1 "/disk1/www/rails/humanrnamap/public/result/3553bd62-7f88-4b7e-ad7c-880b43a0fdf5/fold_dbn/ITCH_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.02 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AUUUGAUCCUCUUGGUCCAUUGCCACCUGGAUGGGAGAAGAGAACAGACAGCAAUGGCAGAGUAUAUUUCGUCAACCACAACACACGAA', '-structureDBN', '...((..((....))..)).(((((.(((..((...........))..)))...)))))........(((((............)))))', '-o', '/disk1/www/rails/humanrnamap/public/result/3553bd62-7f88-4b7e-ad7c-880b43a0fdf5/final_image/ITCH_fold_1.svg', '-title', 'ITCH, -15.4 ± 1.4\n kcal/mol, AUC: 0.703', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,4,5,7,10,12,13,14,15,16,20,21,22,28,29,30,32,33,34,35,37,40,42,47,51,55,56,57,60,62,63,65,67,68,69,71,72,87', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '81,19,23,24,89,58,27', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '70,8,9,77,78,17,18,52,53,85,88,26', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,1,66,6,73,74,11,75,76,79,80,82,83,84,86,25,31,36,38,39,41,43,44,45,46,48,49,50,54,59,61']
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Text: '40', X: 29.286246065769113, Y: 8.0, Width: 18.0, Height: 8
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Text: 'ITCH, -15.4 ± 1.4
 kcal/mol, AUC: 0.703', X: 122.70643667333565, Y: 333.7525365021355, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 383.1628733466713, 333.7525365021355)
Updated viewBox: -0.25 -5.0 388.4128733466713 343.7525365021355
Updated SVG: /disk1/www/rails/humanrnamap/public/result/3553bd62-7f88-4b7e-ad7c-880b43a0fdf5/final_image/ITCH_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/3553bd62-7f88-4b7e-ad7c-880b43a0fdf5/final_image/ITCH_fold_final_1.svg
