Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 94% [================================================  ] \                     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/23832af4-c8c0-4bca-9f75-57aef8353f95/final_image/ITCH_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.44 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.44 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.44 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: ITCH(+)
write fasta - Elapsed time since the previous call: 0.60 seconds
write fasta - Current memory usage: 173.09 MB
Length of region: 95 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: 0.21 seconds
write dat - Current memory usage: 176.48 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/23832af4-c8c0-4bca-9f75-57aef8353f95/fasta/ITCH.fasta" "/disk1/www/rails/humanrnamap/public/result/23832af4-c8c0-4bca-9f75-57aef8353f95/ct/ITCH.ct" --SHAPE "ITCH.dat"

fold - Elapsed time since the previous call: 0.13 seconds
fold - Current memory usage: 176.48 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/23832af4-c8c0-4bca-9f75-57aef8353f95/ct/ITCH.ct" "/disk1/www/rails/humanrnamap/public/result/23832af4-c8c0-4bca-9f75-57aef8353f95/fold_FE/ITCH.txt" -sh "ITCH.dat"

efn2 - Elapsed time since the previous call: 0.42 seconds
efn2 - Current memory usage: 176.48 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/23832af4-c8c0-4bca-9f75-57aef8353f95/ct/ITCH.ct" 1 "/disk1/www/rails/humanrnamap/public/result/23832af4-c8c0-4bca-9f75-57aef8353f95/fold_dbn/ITCH_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.48 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CCUCUUACUAUAUCUGGAGGCUCAGGCCCUAGGCCAUUAAAUCCUGUAACUCAAGCUCCCUUGCCACCUGGUUGGGAGCAGAGAGUGGACCAGCA', '-structureDBN', '(((((..........)))))....((((...))))........((((.((((..((((((..(((....))).))))))...))))..).)))..', '-o', '/disk1/www/rails/humanrnamap/public/result/23832af4-c8c0-4bca-9f75-57aef8353f95/final_image/ITCH_fold_1.svg', '-title', 'ITCH, -38.6 ± 1.2\n kcal/mol, AUC: 0.929', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,5,6,9,11,13,15,16,17,19,20,22,25,26,30,32,33,37,38,42,45,46,47,51,55,57,61,62,63,69,70,71,72,73,74,75,76,78,81,83,85,86,87,88,93', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '65,2,35,59,91,77,79,18,56,58,27,60', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '64,1,4,7,12,14,84,90,92,28,29,34,40,43,44,49,50,52', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '66,67,68,8,10,80,82,21,23,24,89,94,31,95,36,39,41,48,53,54']
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Text: 'C', X: 144.48390186113588, Y: 268.69260103185286, Width: 10.5, Height: 8
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Text: 'C', X: 144.48390186113588, Y: 248.6926010318529, Width: 10.5, Height: 8
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Text: 'U', X: 160.73390186113588, Y: 222.74077518642633, Width: 10.5, Height: 8
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Text: 'G', X: 176.98390186113588, Y: 268.69260103185286, Width: 10.5, Height: 8
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Text: 'C', X: 176.98390186113588, Y: 308.69260103185286, Width: 10.5, Height: 8
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Text: 'U', X: 211.98390186113588, Y: 308.69260103185286, Width: 10.5, Height: 8
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Text: 'U', X: 229.48390186113588, Y: 308.69260103185286, Width: 10.5, Height: 8
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Text: 'A', X: 246.9839018611359, Y: 308.69260103185286, Width: 10.5, Height: 8
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Text: 'A', X: 264.4839018611359, Y: 308.6926010318529, Width: 10.5, Height: 8
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Text: 'A', X: 281.9839018611359, Y: 308.6926010318529, Width: 10.5, Height: 8
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Text: 'U', X: 299.4839018611359, Y: 308.6926010318529, Width: 10.5, Height: 8
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Text: 'C', X: 316.9839018611359, Y: 308.6926010318529, Width: 10.5, Height: 8
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Text: 'C', X: 334.4839018611359, Y: 308.6926010318529, Width: 10.5, Height: 8
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Text: 'U', X: 334.4839018611359, Y: 288.6926010318529, Width: 10.5, Height: 8
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Text: 'G', X: 334.4839018611359, Y: 268.6926010318529, Width: 10.5, Height: 8
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Text: 'A', X: 311.71466137651817, Y: 224.63871638952853, Width: 10.5, Height: 8
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Text: 'U', X: 283.43039012905626, Y: 196.3544451420666, Width: 10.5, Height: 8
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Text: 'C', X: 269.2882545053253, Y: 182.21230951833564, Width: 10.5, Height: 8
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Text: 'A', X: 251.82214390522137, Y: 181.1244217406972, Width: 10.5, Height: 8
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Text: 'A', X: 237.79343243231267, Y: 170.66288391293608, Width: 10.5, Height: 8
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Text: 'C', X: 179.00213011336527, Y: 125.67188192946134, Width: 10.5, Height: 8
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Text: 'G', X: 109.01855923986585, Y: 80.67552796867369, Width: 10.5, Height: 8
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Text: 'C', X: 94.8764236161349, Y: 66.5333923449428, Width: 10.5, Height: 8
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Text: 'C', X: 76.69839561656332, Y: 13.0, Width: 10.5, Height: 8
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Text: 'U', X: 94.10729630093164, Y: 14.783655952920526, Width: 10.5, Height: 8
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Text: 'G', X: 103.71525838096672, Y: 29.41028633264898, Width: 10.5, Height: 8
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Text: 'U', X: 149.5551600140865, Y: 62.63176469210981, Width: 10.5, Height: 8
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Text: 'G', X: 159.29517341848774, Y: 78.04955672555906, Width: 10.5, Height: 8
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Text: 'G', X: 176.88390819060575, Y: 87.56987232516434, Width: 10.5, Height: 8
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Text: 'A', X: 306.4113605176191, Y: 173.37347475350379, Width: 10.5, Height: 8
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Warning: Font Verdana not found. Using default font.
Text: 'A', X: 366.9839018611359, Y: 288.6926010318529, Width: 10.5, Height: 8
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Text: 'G', X: 366.9839018611359, Y: 308.6926010318529, Width: 10.5, Height: 8
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Text: 'C', X: 384.4839018611359, Y: 308.6926010318529, Width: 10.5, Height: 8
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Text: 'A', X: 401.9839018611359, Y: 308.6926010318529, Width: 10.5, Height: 8
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Text: '1', X: 25.233901861135877, Y: 328.69260103185286, Width: 9.0, Height: 8
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Text: '10', X: 23.41363532193492, Y: 141.58237187135538, Width: 18.0, Height: 8
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Text: '20', X: 67.37603748486683, Y: 322.8347366555838, Width: 18.0, Height: 8
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Text: '30', X: 156.98390186113588, Y: 202.74077518642633, Width: 18.0, Height: 8
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Text: '40', X: 260.7339018611359, Y: 328.6926010318529, Width: 18.0, Height: 8
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Text: '50', X: 279.68039012905626, Y: 224.63871638952855, Width: 18.0, Height: 8
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Text: '60', X: 132.32273119284494, Y: 125.0678336822271, Width: 18.0, Height: 8
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Text: '70', X: 112.3162567998645, Y: 13.679652586471263, Width: 18.0, Height: 8
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Text: '80', X: 261.7828865404666, Y: 101.75009152037796, Width: 18.0, Height: 8
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Text: '90', X: 386.5683649471244, Y: 247.25298221400197, Width: 18.0, Height: 8
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Text: '95', X: 398.2339018611359, Y: 328.6926010318529, Width: 18.0, Height: 8
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Text: 'ITCH, -38.6 ± 1.2
 kcal/mol, AUC: 0.929', X: 137.36695093056795, Y: 341.4926010318529, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 416.2339018611359, 341.4926010318529)
Updated viewBox: -0.25 0.0 421.4839018611359 346.4926010318529
Updated SVG: /disk1/www/rails/humanrnamap/public/result/23832af4-c8c0-4bca-9f75-57aef8353f95/final_image/ITCH_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/23832af4-c8c0-4bca-9f75-57aef8353f95/final_image/ITCH_fold_final_1.svg
