Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
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 96% [================================================= ] /                     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/64b18b49-3b92-44ac-a3e3-9a7a7efb0ff6/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: 0.09 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: 83 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: 175.99 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/64b18b49-3b92-44ac-a3e3-9a7a7efb0ff6/fasta/SON.fasta" "/disk1/www/rails/humanrnamap/public/result/64b18b49-3b92-44ac-a3e3-9a7a7efb0ff6/ct/SON.ct" --SHAPE "SON.dat"

fold - Elapsed time since the previous call: 0.09 seconds
fold - Current memory usage: 175.99 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/64b18b49-3b92-44ac-a3e3-9a7a7efb0ff6/ct/SON.ct" "/disk1/www/rails/humanrnamap/public/result/64b18b49-3b92-44ac-a3e3-9a7a7efb0ff6/fold_FE/SON.txt" -sh "SON.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 175.99 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/64b18b49-3b92-44ac-a3e3-9a7a7efb0ff6/ct/SON.ct" 1 "/disk1/www/rails/humanrnamap/public/result/64b18b49-3b92-44ac-a3e3-9a7a7efb0ff6/fold_dbn/SON_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.99 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CACAUCUUAGAAACUCUGAAGCCAGCUACAAAAACUGCAGAACUGUCAGUUGUAUCUACAUCAGUAAUCUCAGAGCAGUCAGA', '-structureDBN', '.............((((((.(...(((.....(((((((....)).)))))...........)))...)))))))........', '-o', '/disk1/www/rails/humanrnamap/public/result/64b18b49-3b92-44ac-a3e3-9a7a7efb0ff6/final_image/SON_fold_1.svg', '-title', 'SON, -9.1 ± 0.8\n kcal/mol, AUC: 0.642', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '5,7,8,10,15,17,18,21,25,27,36,37,40,44,45,46,49,50,51,52,53,55,57,61,64,65,68,70,73,75,78,79,82', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '34,35,42,13,30', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '32,33,4,6,38,39,72,77,14,16,80,81,24,60', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,2,3,66,67,69,71,9,74,11,12,76,19,20,83,22,23,26,28,29,31,41,43,47,48,54,56,58,59,62,63']
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Text: 'C', X: 378.9677147412139, Y: 184.57686730975342, Width: 10.5, Height: 8
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Text: 'A', X: 299.75, Y: 467.43368322919497, Width: 10.5, Height: 8
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Text: 'G', X: 317.25, Y: 467.43368322919497, Width: 10.5, Height: 8
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Text: 'SON, -9.1 ± 0.8
 kcal/mol, AUC: 0.642', X: 138.75, Y: 500.233683229195, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 419.0, 500.233683229195)
Updated viewBox: -0.25 0.0 424.25 505.233683229195
Updated SVG: /disk1/www/rails/humanrnamap/public/result/64b18b49-3b92-44ac-a3e3-9a7a7efb0ff6/final_image/SON_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/64b18b49-3b92-44ac-a3e3-9a7a7efb0ff6/final_image/SON_fold_final_1.svg
