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/07de4301-33bf-4202-be23-b1533b456c11/final_image/SON_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.80 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.80 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.80 MB
read annotations - Elapsed time since the previous call: 0.10 seconds
read annotations - Current memory usage: 172.42 MB
Based on canonical annotations, the following gene is in your area of interest: SON(+)
write fasta - Elapsed time since the previous call: 0.13 seconds
write fasta - Current memory usage: 172.42 MB
Length of region: 84 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: 0.19 seconds
write dat - Current memory usage: 175.84 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/07de4301-33bf-4202-be23-b1533b456c11/fasta/SON.fasta" "/disk1/www/rails/humanrnamap/public/result/07de4301-33bf-4202-be23-b1533b456c11/ct/SON.ct" --SHAPE "SON.dat"

fold - Elapsed time since the previous call: 0.10 seconds
fold - Current memory usage: 175.84 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/07de4301-33bf-4202-be23-b1533b456c11/ct/SON.ct" "/disk1/www/rails/humanrnamap/public/result/07de4301-33bf-4202-be23-b1533b456c11/fold_FE/SON.txt" -sh "SON.dat"

efn2 - Elapsed time since the previous call: 0.51 seconds
efn2 - Current memory usage: 175.84 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/07de4301-33bf-4202-be23-b1533b456c11/ct/SON.ct" 1 "/disk1/www/rails/humanrnamap/public/result/07de4301-33bf-4202-be23-b1533b456c11/fold_dbn/SON_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.84 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CCAUGUGUGCUAAGGCUGGUGUCCCUUUACCACCAAACCUAAAGCCUGCACCUCCACCUACUAUAGAAGAGAAAGUUGCUAAAA', '-structureDBN', '......((((..(((((((((.........))))........)))))))))(((..............))).............', '-o', '/disk1/www/rails/humanrnamap/public/result/07de4301-33bf-4202-be23-b1533b456c11/final_image/SON_fold_1.svg', '-title', 'SON, -16.0 ± 1.2\n kcal/mol, AUC: 0.864', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '4,5,6,7,8,9,11,14,15,17,18,19,20,21,22,26,27,28,40,44,47,48,53,59,62,64,66,69,71,75,76,77,78,80', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '32,34,10,43,46,16,81,31', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '35,39,45,49,51,52,55,58', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,2,3,12,13,23,24,25,29,30,33,36,37,38,41,42,50,54,56,57,60,61,63,65,67,68,70,72,73,74,79,82,83,84']
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Text: 'C', X: 142.25, Y: 279.15189226791847, Width: 10.5, Height: 8
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Text: 'C', X: 159.75, Y: 239.15189226791853, Width: 10.5, Height: 8
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Text: 'C', X: 144.71097477612403, Y: 230.20328470541813, Width: 10.5, Height: 8
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Text: 'A', X: 133.95487307065656, Y: 216.39907762592037, Width: 10.5, Height: 8
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Text: 'U', X: 138.07467572194338, Y: 166.4641958962209, Width: 10.5, Height: 8
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Text: 'A', X: 150.94772870953304, Y: 154.60947684553378, Width: 10.5, Height: 8
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Text: 'G', X: 192.25, Y: 279.15189226791847, Width: 10.5, Height: 8
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Text: 'G', X: 262.25, Y: 279.1518922679185, Width: 10.5, Height: 8
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Text: 'U', X: 279.75, Y: 279.1518922679185, Width: 10.5, Height: 8
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Text: 'U', X: 297.25, Y: 279.1518922679185, Width: 10.5, Height: 8
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Text: 'G', X: 314.75, Y: 279.1518922679185, Width: 10.5, Height: 8
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Text: 'C', X: 332.25, Y: 279.1518922679185, Width: 10.5, Height: 8
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Text: 'U', X: 349.75, Y: 279.1518922679185, Width: 10.5, Height: 8
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Text: 'A', X: 367.25, Y: 279.1518922679185, Width: 10.5, Height: 8
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Text: 'A', X: 419.75, Y: 279.1518922679185, Width: 10.5, Height: 8
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Text: '50', X: 158.5, Y: 259.15189226791847, Width: 18.0, Height: 8
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Text: '70', X: 208.5, Y: 259.15189226791847, Width: 18.0, Height: 8
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Text: '80', X: 346.0, Y: 299.1518922679185, Width: 18.0, Height: 8
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Text: '84', X: 416.0, Y: 299.1518922679185, Width: 18.0, Height: 8
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Text: 'SON, -16.0 ± 1.2
 kcal/mol, AUC: 0.864', X: 146.25, Y: 311.95189226791854, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 434.0, 311.95189226791854)
Updated viewBox: -0.25 0.0 439.25 316.95189226791854
Updated SVG: /disk1/www/rails/humanrnamap/public/result/07de4301-33bf-4202-be23-b1533b456c11/final_image/SON_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/07de4301-33bf-4202-be23-b1533b456c11/final_image/SON_fold_final_1.svg
