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/9212e289-0fad-42d9-b463-0b72e315c044/final_image/ITCH_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.49 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.49 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.49 MB
read annotations - Elapsed time since the previous call: 0.10 seconds
read annotations - Current memory usage: 173.13 MB
Based on canonical annotations, the following gene is in your area of interest: ITCH(+)
write fasta - Elapsed time since the previous call: 0.59 seconds
write fasta - Current memory usage: 173.13 MB
Length of region: 100 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: 176.52 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/9212e289-0fad-42d9-b463-0b72e315c044/fasta/ITCH.fasta" "/disk1/www/rails/humanrnamap/public/result/9212e289-0fad-42d9-b463-0b72e315c044/ct/ITCH.ct" --SHAPE "ITCH.dat"

fold - Elapsed time since the previous call: 0.12 seconds
fold - Current memory usage: 176.52 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/9212e289-0fad-42d9-b463-0b72e315c044/ct/ITCH.ct" "/disk1/www/rails/humanrnamap/public/result/9212e289-0fad-42d9-b463-0b72e315c044/fold_FE/ITCH.txt" -sh "ITCH.dat"

efn2 - Elapsed time since the previous call: 0.43 seconds
efn2 - Current memory usage: 176.52 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/9212e289-0fad-42d9-b463-0b72e315c044/ct/ITCH.ct" 1 "/disk1/www/rails/humanrnamap/public/result/9212e289-0fad-42d9-b463-0b72e315c044/fold_dbn/ITCH_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.52 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CGGGCGAGUUUACUAUGUAGAUCAUGUUGAGAAAAGAACAACAUGGGAUAGACCAGAACCUCUACCUCCUGGCUGGGAACGGCGGGUUGACAACAUGGGA', '-structureDBN', '.((..((((((......((..((((((((.........))))))))..)).....))).)))..)).(((.((((....)))))))..............', '-o', '/disk1/www/rails/humanrnamap/public/result/9212e289-0fad-42d9-b463-0b72e315c044/final_image/ITCH_fold_1.svg', '-title', 'ITCH, -28.8 ± 1.1\n kcal/mol, AUC: 0.856', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,4,6,8,9,10,11,14,16,17,18,20,22,25,26,27,28,29,31,36,44,45,46,47,49,51,56,61,63,67,70,71,72,74,75,76,77,81,82,84,85,86,87,88,89,96,97,98,99', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '66,68,69,40,41,42,43,73,24', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '33,65,100,39,48,50,19,83,54,23,60', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,1,5,7,12,13,78,15,79,80,21,90,91,92,93,30,94,32,95,34,35,37,38,52,53,55,57,58,59,62']
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Text: '20', X: 41.222661603832, Y: 257.55974396707376, Width: 18.0, Height: 8
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Text: '30', X: -4.0, Y: 83.59500998040954, Width: 18.0, Height: 8
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Text: '40', X: 81.11539837274319, Y: 84.28510092525539, Width: 18.0, Height: 8
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Text: '50', X: 123.72444444794249, Y: 256.6003161381523, Width: 18.0, Height: 8
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Text: '70', X: 175.8780465685214, Y: 479.3931292462793, Width: 18.0, Height: 8
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Text: '80', X: 276.5936558742856, Y: 416.50063354579936, Width: 18.0, Height: 8
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Text: '100', X: 468.7573859423278, Y: 541.5867258502683, Width: 27.0, Height: 8
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Text: 'ITCH, -28.8 ± 1.1
 kcal/mol, AUC: 0.856', X: 175.01238795380547, Y: 554.3867258502682, Width: 142.5, Height: 23
Calculated bounding box: (-4.0, 5.0, 495.7573859423278, 554.3867258502682)
Updated viewBox: -9.0 0.0 509.7573859423278 559.3867258502682
Updated SVG: /disk1/www/rails/humanrnamap/public/result/9212e289-0fad-42d9-b463-0b72e315c044/final_image/ITCH_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/9212e289-0fad-42d9-b463-0b72e315c044/final_image/ITCH_fold_final_1.svg
