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/060ba34a-410b-4a56-b9cf-51ac4055d8f1/final_image/CALD1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.02 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.02 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.02 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 171.52 MB
Based on canonical annotations, the following gene is in your area of interest: CALD1(+)
write fasta - Elapsed time since the previous call: 0.81 seconds
write fasta - Current memory usage: 171.52 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: 0.16 seconds
write dat - Current memory usage: 175.00 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/060ba34a-410b-4a56-b9cf-51ac4055d8f1/fasta/CALD1.fasta" "/disk1/www/rails/humanrnamap/public/result/060ba34a-410b-4a56-b9cf-51ac4055d8f1/ct/CALD1.ct" --SHAPE "CALD1.dat"

fold - Elapsed time since the previous call: 0.08 seconds
fold - Current memory usage: 175.00 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/060ba34a-410b-4a56-b9cf-51ac4055d8f1/ct/CALD1.ct" "/disk1/www/rails/humanrnamap/public/result/060ba34a-410b-4a56-b9cf-51ac4055d8f1/fold_FE/CALD1.txt" -sh "CALD1.dat"

efn2 - Elapsed time since the previous call: 0.42 seconds
efn2 - Current memory usage: 175.00 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/060ba34a-410b-4a56-b9cf-51ac4055d8f1/ct/CALD1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/060ba34a-410b-4a56-b9cf-51ac4055d8f1/fold_dbn/CALD1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.00 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CUGAAGAAAACAAGAAAGAAGACAAGGAAAAGGAGGAGGAGGAAGAGGAGAAGCCAAAGCGAGGGAGCAUUGGAGAAAAUCAGA', '-structureDBN', '.....................................................((((.((......)).))))...........', '-o', '/disk1/www/rails/humanrnamap/public/result/060ba34a-410b-4a56-b9cf-51ac4055d8f1/final_image/CALD1_fold_1.svg', '-title', 'CALD1, -5.9 ± 0.4\n kcal/mol, AUC: 0.436', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,6,14,18,21,26,27,32,33,35,36,38,39,41,42,45,47,48,50,53,59,61,63,64,65,67,70,71,72,73,75,80,83', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '28,51,8,56,44,77', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '66,68,7,9,10,74,76,17,82,20,84,22,29,40,43,52,55', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,4,5,69,11,12,13,78,15,16,79,81,19,23,24,25,30,31,34,37,46,49,54,57,58,60,62']
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Text: 'C', X: 932.25, Y: 148.97443252442042, Width: 10.5, Height: 8
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Text: 'A', X: 932.25, Y: 128.97443252442042, Width: 10.5, Height: 8
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Text: 'A', X: 925.5716228485107, Y: 92.79889609433768, Width: 10.5, Height: 8
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Text: 'A', X: 973.5969000915029, Y: 41.52430305167013, Width: 10.5, Height: 8
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Text: 'G', X: 964.75, Y: 56.623359664254906, Width: 10.5, Height: 8
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Text: 'A', X: 971.4283771514893, Y: 92.79889609433768, Width: 10.5, Height: 8
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Text: 'U', X: 964.75, Y: 108.97443252442044, Width: 10.5, Height: 8
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Text: 'U', X: 964.75, Y: 128.97443252442042, Width: 10.5, Height: 8
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Text: 'G', X: 999.75, Y: 168.97443252442042, Width: 10.5, Height: 8
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Text: 'A', X: 1017.25, Y: 168.97443252442042, Width: 10.5, Height: 8
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Text: 'A', X: 1034.75, Y: 168.97443252442042, Width: 10.5, Height: 8
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Text: 'U', X: 1087.25, Y: 168.97443252442045, Width: 10.5, Height: 8
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Text: 'C', X: 1104.75, Y: 168.97443252442045, Width: 10.5, Height: 8
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Text: 'A', X: 1122.25, Y: 168.97443252442045, Width: 10.5, Height: 8
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Text: '10', X: 158.5, Y: 188.9744325244204, Width: 18.0, Height: 8
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Text: '20', X: 333.5, Y: 188.9744325244204, Width: 18.0, Height: 8
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Text: '30', X: 508.5, Y: 188.97443252442042, Width: 18.0, Height: 8
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Text: '40', X: 683.5, Y: 188.97443252442042, Width: 18.0, Height: 8
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Text: '50', X: 858.5, Y: 188.97443252442042, Width: 18.0, Height: 8
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Text: '70', X: 981.0, Y: 108.97443252442044, Width: 18.0, Height: 8
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Text: '84', X: 1153.5, Y: 188.97443252442045, Width: 18.0, Height: 8
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Text: 'CALD1, -5.9 ± 0.4
 kcal/mol, AUC: 0.436', X: 515.0, Y: 201.77443252442046, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 1171.5, 201.77443252442046)
Updated viewBox: -0.25 0.0 1176.75 206.77443252442046
Updated SVG: /disk1/www/rails/humanrnamap/public/result/060ba34a-410b-4a56-b9cf-51ac4055d8f1/final_image/CALD1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/060ba34a-410b-4a56-b9cf-51ac4055d8f1/final_image/CALD1_fold_final_1.svg
