Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 97% [================================================= ] |                     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/84f2098d-516f-4d5e-ac4e-19569d7fd4bc/final_image/ITCH_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.90 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.90 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.90 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.52 MB
Based on canonical annotations, the following gene is in your area of interest: ITCH(+)
write fasta - Elapsed time since the previous call: 0.57 seconds
write fasta - Current memory usage: 172.52 MB
Length of region: 97 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: 176.06 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/84f2098d-516f-4d5e-ac4e-19569d7fd4bc/fasta/ITCH.fasta" "/disk1/www/rails/humanrnamap/public/result/84f2098d-516f-4d5e-ac4e-19569d7fd4bc/ct/ITCH.ct" --SHAPE "ITCH.dat"

fold - Elapsed time since the previous call: 0.13 seconds
fold - Current memory usage: 176.06 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/84f2098d-516f-4d5e-ac4e-19569d7fd4bc/ct/ITCH.ct" "/disk1/www/rails/humanrnamap/public/result/84f2098d-516f-4d5e-ac4e-19569d7fd4bc/fold_FE/ITCH.txt" -sh "ITCH.dat"

efn2 - Elapsed time since the previous call: 0.54 seconds
efn2 - Current memory usage: 176.06 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/84f2098d-516f-4d5e-ac4e-19569d7fd4bc/ct/ITCH.ct" 1 "/disk1/www/rails/humanrnamap/public/result/84f2098d-516f-4d5e-ac4e-19569d7fd4bc/fold_dbn/ITCH_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 176.06 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CAGAUAGCCUAUGUUCGGGACUUCAAAGCAAAGGUUCAGUAUUUCCGGUUCUGGUGUCAGCAACUGGCCAUGCCACAGCACAUAAAGAUUACAGUGA', '-structureDBN', '.....(((((.((((..((...))..)))).)))))..((((..(((((((((....))).))))))..))))(((.................))).', '-o', '/disk1/www/rails/humanrnamap/public/result/84f2098d-516f-4d5e-ac4e-19569d7fd4bc/final_image/ITCH_fold_1.svg', '-title', 'ITCH, -24.2 ± 1.2\n kcal/mol, AUC: 0.667', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,5,7,10,12,13,14,15,17,18,19,22,23,28,33,34,35,36,39,40,42,43,44,47,48,49,50,52,53,54,55,56,57,60,65,66,67,71,72,78,83,87,89,90,94,95,96', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '2,8,9,73,74,75,45,51,58,59,63', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '32,1,97,69,38,91,11,46,20,62,26,88,61,30', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,4,68,6,70,76,77,79,16,80,81,82,84,21,85,86,24,25,27,92,29,93,31,37,41']
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Text: 'C', X: 177.25, Y: 184.70346077421993, Width: 10.5, Height: 8
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Text: 'C', X: 173.43439675932206, Y: 87.6243591710641, Width: 10.5, Height: 8
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Text: 'C', X: 220.12968331740177, Y: 218.79289999535104, Width: 10.5, Height: 8
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Text: 'C', X: 220.12968331740177, Y: 236.29290351922197, Width: 10.5, Height: 8
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Text: 'A', X: 209.75, Y: 250.38234274035307, Width: 10.5, Height: 8
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Text: 'U', X: 209.75, Y: 270.38234274035307, Width: 10.5, Height: 8
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Text: 'G', X: 209.75, Y: 290.382342740353, Width: 10.5, Height: 8
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Text: 'C', X: 209.75, Y: 310.382342740353, Width: 10.5, Height: 8
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Text: 'C', X: 227.25, Y: 310.382342740353, Width: 10.5, Height: 8
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Text: 'A', X: 227.25, Y: 290.382342740353, Width: 10.5, Height: 8
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Text: 'C', X: 227.25, Y: 270.38234274035307, Width: 10.5, Height: 8
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Text: 'A', X: 211.5280312146983, Y: 262.6966072820843, Width: 10.5, Height: 8
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Text: 'G', X: 198.97428640652726, Y: 250.50421935716128, Width: 10.5, Height: 8
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Text: 'C', X: 190.83276389073328, Y: 235.01336905302014, Width: 10.5, Height: 8
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Text: 'A', X: 187.9102380958197, Y: 217.7591036383885, Width: 10.5, Height: 8
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Text: 'U', X: 259.75, Y: 290.38234274035307, Width: 10.5, Height: 8
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Text: 'G', X: 259.75, Y: 310.38234274035307, Width: 10.5, Height: 8
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Text: '1', X: 5.5, Y: 330.382342740353, Width: 9.0, Height: 8
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Text: '10', X: 68.5, Y: 230.38234274035304, Width: 18.0, Height: 8
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Text: '20', X: 72.48907978138166, Y: 44.26352278949571, Width: 18.0, Height: 8
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Text: '30', X: 141.0, Y: 198.0312698801875, Width: 18.0, Height: 8
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Text: '40', X: 153.5, Y: 290.382342740353, Width: 18.0, Height: 8
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Text: '50', X: 153.5, Y: 104.70346077421999, Width: 18.0, Height: 8
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Text: '60', X: 218.0172116257087, Y: 67.3180469779133, Width: 18.0, Height: 8
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Text: '70', X: 225.74856510286514, Y: 253.5436994709193, Width: 18.0, Height: 8
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Text: '80', X: 164.16118566364918, Y: 217.95378752394328, Width: 18.0, Height: 8
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Text: '90', X: 315.3388143363508, Y: 217.95378752394325, Width: 18.0, Height: 8
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Text: '97', X: 273.5, Y: 330.38234274035307, Width: 18.0, Height: 8
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Text: 'ITCH, -24.2 ± 1.2
 kcal/mol, AUC: 0.667', X: 85.91988095209015, Y: 343.1823427403531, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 333.3388143363508, 343.1823427403531)
Updated viewBox: -0.25 0.0 338.5888143363508 348.1823427403531
Updated SVG: /disk1/www/rails/humanrnamap/public/result/84f2098d-516f-4d5e-ac4e-19569d7fd4bc/final_image/ITCH_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/84f2098d-516f-4d5e-ac4e-19569d7fd4bc/final_image/ITCH_fold_final_1.svg
