Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  6% [====                                              ] -                     
 12% [=======                                           ] \                     
 18% [==========                                        ] |                     
 25% [=============                                     ] /                     
 31% [================                                  ] -                     
 37% [===================                               ] \                     
 43% [======================                            ] |                     
 50% [==========================                        ] /                     
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 62% [================================                  ] \                     
 68% [===================================               ] |                     
 75% [======================================            ] /                     
 81% [=========================================         ] -                     
 87% [============================================      ] \                     
 93% [===============================================   ] |                     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/e225ff22-f375-4dac-8d4d-0fb6fd1f1fed/final_image/SON_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.04 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.04 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.04 MB
read annotations - Elapsed time since the previous call: 0.10 seconds
read annotations - Current memory usage: 172.66 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: 172.66 MB
Length of region: 80 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: 176.18 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/e225ff22-f375-4dac-8d4d-0fb6fd1f1fed/fasta/SON.fasta" "/disk1/www/rails/humanrnamap/public/result/e225ff22-f375-4dac-8d4d-0fb6fd1f1fed/ct/SON.ct" --SHAPE "SON.dat"

fold - Elapsed time since the previous call: 0.09 seconds
fold - Current memory usage: 176.18 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/e225ff22-f375-4dac-8d4d-0fb6fd1f1fed/ct/SON.ct" "/disk1/www/rails/humanrnamap/public/result/e225ff22-f375-4dac-8d4d-0fb6fd1f1fed/fold_FE/SON.txt" -sh "SON.dat"

efn2 - Elapsed time since the previous call: 0.45 seconds
efn2 - Current memory usage: 176.18 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/e225ff22-f375-4dac-8d4d-0fb6fd1f1fed/ct/SON.ct" 1 "/disk1/www/rails/humanrnamap/public/result/e225ff22-f375-4dac-8d4d-0fb6fd1f1fed/fold_dbn/SON_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.18 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AAUGCCACCGUUGCCACCUGAGGAGCCACCAAUGACACCACCAUUGCCUCCUGAGGAACCACCAGAGGGUCCAGCAUUGC', '-structureDBN', '(((((.(((.((....(((.(((((....(((((.......))))).))))).)))........)).)))...)))))..', '-o', '/disk1/www/rails/humanrnamap/public/result/e225ff22-f375-4dac-8d4d-0fb6fd1f1fed/final_image/SON_fold_1.svg', '-title', 'SON, -24.1 ± 1.2\n kcal/mol, AUC: 0.713', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '65,3,4,67,68,69,70,10,11,12,13,74,77,78,79,19,20,22,23,25,33,34,44,45,46,49,52,53,55,56', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '6,7,39,72,48,18,50,51,21,24,27,31', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '64,1,66,73,15,80,17,30,32,35,37,40,43,54,57,60,61,63', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '2,5,71,8,9,75,76,14,16,26,28,29,36,38,41,42,47,58,59,62']
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Text: 'G', X: 351.961461039411, Y: 235.96135397723037, Width: 10.5, Height: 8
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Text: 'C', X: 423.45082686688545, Y: 381.1801798111764, Width: 10.5, Height: 8
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Text: 'A', X: 423.45082686688545, Y: 401.1801798111764, Width: 10.5, Height: 8
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Text: 'U', X: 423.45082686688545, Y: 421.1801798111764, Width: 10.5, Height: 8
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Text: 'U', X: 423.45082686688545, Y: 441.1801798111764, Width: 10.5, Height: 8
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Text: 'C', X: 458.45082686688545, Y: 441.1801798111764, Width: 10.5, Height: 8
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Text: '40', X: 62.956121321762254, Y: 8.0, Width: 18.0, Height: 8
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Text: '50', X: 160.24083574461335, Y: 136.3567969480594, Width: 18.0, Height: 8
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Text: '80', X: 454.70082686688545, Y: 461.1801798111764, Width: 18.0, Height: 8
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Text: 'SON, -24.1 ± 1.2
 kcal/mol, AUC: 0.713', X: 165.60041343344272, Y: 473.9801798111764, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 472.70082686688545, 473.9801798111764)
Updated viewBox: -0.25 -5.0 477.95082686688545 483.9801798111764
Updated SVG: /disk1/www/rails/humanrnamap/public/result/e225ff22-f375-4dac-8d4d-0fb6fd1f1fed/final_image/SON_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/e225ff22-f375-4dac-8d4d-0fb6fd1f1fed/final_image/SON_fold_final_1.svg
