Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 98% [==================================================] |                     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/b7175038-a88d-40ed-8873-269098c7b808/final_image/SON_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.73 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.73 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.73 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.46 MB
Based on canonical annotations, the following gene is in your area of interest: SON(+)
write fasta - Elapsed time since the previous call: 0.14 seconds
write fasta - Current memory usage: 172.46 MB
Length of region: 96 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: 0.17 seconds
write dat - Current memory usage: 176.03 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/b7175038-a88d-40ed-8873-269098c7b808/fasta/SON.fasta" "/disk1/www/rails/humanrnamap/public/result/b7175038-a88d-40ed-8873-269098c7b808/ct/SON.ct" --SHAPE "SON.dat"

fold - Elapsed time since the previous call: 0.12 seconds
fold - Current memory usage: 176.03 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/b7175038-a88d-40ed-8873-269098c7b808/ct/SON.ct" "/disk1/www/rails/humanrnamap/public/result/b7175038-a88d-40ed-8873-269098c7b808/fold_FE/SON.txt" -sh "SON.dat"

efn2 - Elapsed time since the previous call: 0.51 seconds
efn2 - Current memory usage: 176.03 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/b7175038-a88d-40ed-8873-269098c7b808/ct/SON.ct" 1 "/disk1/www/rails/humanrnamap/public/result/b7175038-a88d-40ed-8873-269098c7b808/fold_dbn/SON_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.03 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CUAUCCUCUGGUGAUCAAAAUCUUGCUCCAGAGAUUGGCAUGCAGGAGAUUGCAUUGCAUUCAGGUGAAGAACCACAUGCUGAGGAACACCUGAAA', '-structureDBN', '.....((((((....(((....)))..))))))....((((((((....))))).))).((((((((.....((.........))..)))))))).', '-o', '/disk1/www/rails/humanrnamap/public/result/b7175038-a88d-40ed-8873-269098c7b808/final_image/SON_fold_1.svg', '-title', 'SON, -38.8 ± 1.2\n kcal/mol, AUC: 0.942', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,4,7,9,10,11,12,13,15,21,23,24,25,27,31,33,35,36,37,38,41,42,45,46,48,50,51,52,55,56,57,60,61,64,65,66,67,70,78,79,81,82,84,85,92,93', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '6,8,74,18,88,89,90,91,28,29,94,30,32,39,40,43,53,63', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '3,58,73,75,44,14,80,17,19,20,22,54,26,62,95', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,68,5,69,71,72,76,77,16,83,86,87,96,34,47,49,59']
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Text: 'A', X: 182.89992122261455, Y: 163.9461728139022, Width: 10.5, Height: 8
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Text: 'G', X: 174.38842937704538, Y: 145.84770584670275, Width: 10.5, Height: 8
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Text: 'A', X: 199.71693535037258, Y: 114.99911152011697, Width: 10.5, Height: 8
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Text: 'U', X: 279.75, Y: 155.32067531865636, Width: 10.5, Height: 8
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Text: 'A', X: 266.338520954835, Y: 123.6309650036439, Width: 10.5, Height: 8
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Text: 'G', X: 262.69255849458557, Y: 89.34255285368641, Width: 10.5, Height: 8
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Text: 'A', X: 273.3459616992245, Y: 75.09397055272763, Width: 10.5, Height: 8
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Text: 'A', X: 289.5162120215337, Y: 67.67506888592624, Width: 10.5, Height: 8
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Text: 'C', X: 307.2654332339627, Y: 68.89254323065205, Width: 10.5, Height: 8
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Text: 'C', X: 321.40756885769366, Y: 54.7504076069211, Width: 10.5, Height: 8
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Text: 'A', X: 321.11752623144787, Y: 37.252826306433064, Width: 10.5, Height: 8
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Text: 'C', X: 329.6714225991109, Y: 21.985857615055295, Width: 10.5, Height: 8
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Text: 'A', X: 344.745641747724, Y: 13.096684810355441, Width: 10.5, Height: 8
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Text: 'U', X: 362.24535969229885, Y: 13.0, Width: 10.5, Height: 8
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Text: 'G', X: 377.4168798026144, Y: 21.722067050563112, Width: 10.5, Height: 8
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Text: 'C', X: 386.13894685317746, Y: 36.89358716087867, Width: 10.5, Height: 8
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Text: 'U', X: 386.042262042822, Y: 54.39330510545352, Width: 10.5, Height: 8
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Text: 'G', X: 377.1530892381222, Y: 69.46752425406663, Width: 10.5, Height: 8
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Text: 'A', X: 361.8861205467445, Y: 78.02142062172965, Width: 10.5, Height: 8
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Text: 'G', X: 312.25, Y: 235.32067531865636, Width: 10.5, Height: 8
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Text: 'A', X: 312.25, Y: 275.32067531865636, Width: 10.5, Height: 8
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Text: 'A', X: 329.75, Y: 275.32067531865636, Width: 10.5, Height: 8
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Text: '1', X: 5.5, Y: 295.3206753186563, Width: 9.0, Height: 8
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Text: '10', X: 68.5, Y: 195.32067531865633, Width: 18.0, Height: 8
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Text: '20', X: 149.49503562998427, Y: 35.75313600813405, Width: 18.0, Height: 8
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Text: '30', X: 141.0, Y: 215.32067531865633, Width: 18.0, Height: 8
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Text: '40', X: 188.5, Y: 235.32067531865636, Width: 18.0, Height: 8
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Text: '50', X: 217.0002185504676, Y: 121.40346687030225, Width: 18.0, Height: 8
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Text: '60', X: 261.85786437626905, Y: 289.4628109423873, Width: 18.0, Height: 8
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Text: '70', X: 240.46496784435982, Y: 81.68888420638461, Width: 18.0, Height: 8
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Text: '80', X: 401.7263982143514, Y: 31.788396189501213, Width: 18.0, Height: 8
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Text: '90', X: 328.5, Y: 175.32067531865636, Width: 18.0, Height: 8
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Text: '96', X: 326.0, Y: 295.32067531865636, Width: 18.0, Height: 8
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Text: 'SON, -38.8 ± 1.2
 kcal/mol, AUC: 0.942', X: 129.44447342658873, Y: 308.12067531865637, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 419.7263982143514, 308.12067531865637)
Updated viewBox: -0.25 0.0 424.9763982143514 313.12067531865637
Updated SVG: /disk1/www/rails/humanrnamap/public/result/b7175038-a88d-40ed-8873-269098c7b808/final_image/SON_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/b7175038-a88d-40ed-8873-269098c7b808/final_image/SON_fold_final_1.svg
