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/986dae23-fcac-4d35-a34a-5451696ffe23/final_image/CALD1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 157.90 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 157.90 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 157.90 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 171.47 MB
Based on canonical annotations, the following gene is in your area of interest: CALD1(+)
write fasta - Elapsed time since the previous call: 0.89 seconds
write fasta - Current memory usage: 171.47 MB
Length of region: 90 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: 0.20 seconds
write dat - Current memory usage: 174.79 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/986dae23-fcac-4d35-a34a-5451696ffe23/fasta/CALD1.fasta" "/disk1/www/rails/humanrnamap/public/result/986dae23-fcac-4d35-a34a-5451696ffe23/ct/CALD1.ct" --SHAPE "CALD1.dat"

fold - Elapsed time since the previous call: 0.12 seconds
fold - Current memory usage: 174.79 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/986dae23-fcac-4d35-a34a-5451696ffe23/ct/CALD1.ct" "/disk1/www/rails/humanrnamap/public/result/986dae23-fcac-4d35-a34a-5451696ffe23/fold_FE/CALD1.txt" -sh "CALD1.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 174.79 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/986dae23-fcac-4d35-a34a-5451696ffe23/ct/CALD1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/986dae23-fcac-4d35-a34a-5451696ffe23/fold_dbn/CALD1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 174.79 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CGAGCAGAAUUUUUGAAUAAGUCUGUGCAGAAAAGCAGUGGUGUCAAAUCGACCCAUCAAGCAGCAAUAGUCUCCAAGAUUGACAGCAGA', '-structureDBN', '...((((.((((......))))))))........((.((((.(((.....)))))))...)).((..((((((...))))))...))...', '-o', '/disk1/www/rails/humanrnamap/public/result/986dae23-fcac-4d35-a34a-5451696ffe23/final_image/CALD1_fold_1.svg', '-title', 'CALD1, -17.0 ± 0.7\n kcal/mol, AUC: 0.783', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,4,7,10,11,12,13,14,15,18,21,22,24,25,26,27,30,35,38,39,40,41,42,43,44,49,51,57,61,64,68,70,71,73,78,80,81,82,86,89', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '8,9,72,45,52,53,54,55,87', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '3,36,74,75,76,46,83,20,56,62', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,65,66,67,5,6,69,77,79,16,17,19,84,85,23,88,90,28,29,31,32,33,34,37,47,48,50,58,59,60,63']
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Text: 'G', X: 279.75, Y: 202.56042780302204, Width: 10.5, Height: 8
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Text: 'C', X: 279.75, Y: 222.56042780302204, Width: 10.5, Height: 8
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Text: 'A', X: 297.25, Y: 222.56042780302204, Width: 10.5, Height: 8
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Text: 'G', X: 314.75, Y: 222.56042780302204, Width: 10.5, Height: 8
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Text: 'C', X: 314.75, Y: 202.56042780302204, Width: 10.5, Height: 8
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Text: 'A', X: 303.16884757845037, Y: 189.44076973199617, Width: 10.5, Height: 8
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Text: 'A', X: 300.6464749042966, Y: 172.1235483785434, Width: 10.5, Height: 8
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Text: 'U', X: 308.00389068569103, Y: 156.24535728725454, Width: 10.5, Height: 8
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Text: 'A', X: 302.2986567753517, Y: 137.0763639378813, Width: 10.5, Height: 8
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Text: 'G', X: 296.59342286501237, Y: 117.90737058850812, Width: 10.5, Height: 8
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Text: 'C', X: 285.18295504433377, Y: 79.56938388976167, Width: 10.5, Height: 8
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Text: 'U', X: 279.47772113399446, Y: 60.40039054038846, Width: 10.5, Height: 8
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Text: 'C', X: 287.6494663879328, Y: 30.891369136484172, Width: 10.5, Height: 8
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Text: '1', X: 5.5, Y: 242.560427803022, Width: 9.0, Height: 8
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Text: '20', X: 124.93727815331562, Y: 117.79626883745709, Width: 18.0, Height: 8
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Text: '30', X: 156.0, Y: 242.56042780302204, Width: 18.0, Height: 8
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Text: '40', X: 193.29313340866668, Y: 150.62901669199698, Width: 18.0, Height: 8
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Text: '50', X: 231.86747672498282, Y: 27.035136539251596, Width: 18.0, Height: 8
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Text: '60', X: 305.38026369557775, Y: 194.71422054078022, Width: 18.0, Height: 8
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Text: '70', X: 273.6744295156392, Y: 123.61260449884745, Width: 18.0, Height: 8
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Text: '80', X: 343.1620304071171, Y: 102.93113157386736, Width: 18.0, Height: 8
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Text: '90', X: 396.0, Y: 242.56042780302204, Width: 18.0, Height: 8
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Text: 'CALD1, -17.0 ± 0.7
 kcal/mol, AUC: 0.783', X: 136.25, Y: 255.36042780302205, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 414.0, 255.36042780302205)
Updated viewBox: -0.25 0.0 419.25 260.36042780302205
Updated SVG: /disk1/www/rails/humanrnamap/public/result/986dae23-fcac-4d35-a34a-5451696ffe23/final_image/CALD1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/986dae23-fcac-4d35-a34a-5451696ffe23/final_image/CALD1_fold_final_1.svg
