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/6689b46e-57d5-445b-9e1c-90b7c14e52c3/final_image/ITCH_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 157.99 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 157.99 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 157.99 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 171.61 MB
Based on canonical annotations, the following gene is in your area of interest: ITCH(+)
write fasta - Elapsed time since the previous call: 0.56 seconds
write fasta - Current memory usage: 171.61 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: 174.73 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/6689b46e-57d5-445b-9e1c-90b7c14e52c3/fasta/ITCH.fasta" "/disk1/www/rails/humanrnamap/public/result/6689b46e-57d5-445b-9e1c-90b7c14e52c3/ct/ITCH.ct" --SHAPE "ITCH.dat"

fold - Elapsed time since the previous call: 0.10 seconds
fold - Current memory usage: 174.73 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/6689b46e-57d5-445b-9e1c-90b7c14e52c3/ct/ITCH.ct" "/disk1/www/rails/humanrnamap/public/result/6689b46e-57d5-445b-9e1c-90b7c14e52c3/fold_FE/ITCH.txt" -sh "ITCH.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 174.73 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/6689b46e-57d5-445b-9e1c-90b7c14e52c3/ct/ITCH.ct" 1 "/disk1/www/rails/humanrnamap/public/result/6689b46e-57d5-445b-9e1c-90b7c14e52c3/fold_dbn/ITCH_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 174.73 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CAUACCUGUUUUAAUCGCCUGGACCUGCCACCAUACAAGAGCUAUGAGCAACUGAAGGAAAAGCUGUUGUUUGCCAUAGAAGAAACAGA', '-structureDBN', '.....(((((((.......(((.....)))...........(((((.(((((...((......))...).)))))))))..))))))).', '-o', '/disk1/www/rails/humanrnamap/public/result/6689b46e-57d5-445b-9e1c-90b7c14e52c3/final_image/ITCH_fold_1.svg', '-title', 'ITCH, -15.0 ± 0.8\n kcal/mol, AUC: 0.716', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,7,8,9,10,11,12,15,17,20,21,22,26,27,34,39,41,43,45,46,48,53,54,57,58,63,65,66,67,68,69,70,71,72,73,77,79,82,88', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '33,49,50,51,59,76,29', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '74,75,13,78,19,84,85,86,23,87,25,28,30,32,35,37,38,42,44,60,62', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,1,2,4,5,6,14,16,80,18,81,83,24,89,31,36,40,47,52,55,56,61']
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Text: 'G', X: 390.79029243695123, Y: 252.74132582141425, Width: 10.5, Height: 8
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Text: 'G', X: 418.9938879534516, Y: 334.87160848097176, Width: 10.5, Height: 8
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Text: 'C', X: 410.0095793466874, Y: 319.8539072361908, Width: 10.5, Height: 8
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Text: 'U', X: 392.47387776513887, Y: 310.23625835286816, Width: 10.5, Height: 8
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Text: 'G', X: 341.402133403517, Y: 282.22541430388094, Width: 10.5, Height: 8
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Text: 'U', X: 324.59268043028624, Y: 277.3579415776355, Width: 10.5, Height: 8
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Text: 'U', X: 317.6212329929082, Y: 261.3064955172995, Width: 10.5, Height: 8
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Text: 'U', X: 305.84578579932094, Y: 245.14051755767585, Width: 10.5, Height: 8
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Text: 'G', X: 294.0703386057337, Y: 228.9745395980522, Width: 10.5, Height: 8
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Text: 'C', X: 282.2948914121465, Y: 212.80856163842853, Width: 10.5, Height: 8
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Text: 'C', X: 269.1550976644095, Y: 201.250195825437, Width: 10.5, Height: 8
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Text: 'C', X: 154.56033653237813, Y: 269.09881915931953, Width: 10.5, Height: 8
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Text: '10', X: 98.31033653237813, Y: 229.0988191593195, Width: 18.0, Height: 8
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Text: '20', X: 42.37895252483236, Y: 88.28145276478182, Width: 18.0, Height: 8
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Text: '30', X: 79.53486795981732, Y: 33.60041573160413, Width: 18.0, Height: 8
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Text: '40', X: 233.3606778527627, Y: 96.7527069206489, Width: 18.0, Height: 8
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Text: '50', X: 344.5314779433331, Y: 214.22996867450928, Width: 18.0, Height: 8
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Text: '60', X: 476.300779242996, Y: 321.9309608065203, Width: 18.0, Height: 8
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Text: '80', X: 194.52316359627818, Y: 190.7523130508819, Width: 18.0, Height: 8
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Text: '89', X: 168.31033653237813, Y: 329.09881915931953, Width: 18.0, Height: 8
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Text: 'ITCH, -15.0 ± 0.8
 kcal/mol, AUC: 0.716', X: 166.51497273844655, Y: 358.3655083500464, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 494.300779242996, 358.3655083500464)
Updated viewBox: -0.25 0.0 499.550779242996 363.3655083500464
Updated SVG: /disk1/www/rails/humanrnamap/public/result/6689b46e-57d5-445b-9e1c-90b7c14e52c3/final_image/ITCH_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/6689b46e-57d5-445b-9e1c-90b7c14e52c3/final_image/ITCH_fold_final_1.svg
