Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  6% [====                                              ] -                     
 12% [=======                                           ] \                     
 18% [==========                                        ] |                     
 25% [=============                                     ] /                     
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 37% [===================                               ] \                     
 44% [=======================                           ] |                     
 50% [==========================                        ] /                     
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 88% [=============================================     ] \                     
 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/3f9e433f-405b-4406-a3ae-cdeb6fa1be0d/final_image/RUNX1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 157.07 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 157.07 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 157.07 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 170.67 MB
Based on canonical annotations, the following gene is in your area of interest: RUNX1(-)
write fasta - Elapsed time since the previous call: 0.25 seconds
write fasta - Current memory usage: 170.67 MB
Length of region: 79 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: 173.72 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/3f9e433f-405b-4406-a3ae-cdeb6fa1be0d/fasta/RUNX1.fasta" "/disk1/www/rails/humanrnamap/public/result/3f9e433f-405b-4406-a3ae-cdeb6fa1be0d/ct/RUNX1.ct" --SHAPE "RUNX1.dat"

fold - Elapsed time since the previous call: 0.08 seconds
fold - Current memory usage: 173.72 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/3f9e433f-405b-4406-a3ae-cdeb6fa1be0d/ct/RUNX1.ct" "/disk1/www/rails/humanrnamap/public/result/3f9e433f-405b-4406-a3ae-cdeb6fa1be0d/fold_FE/RUNX1.txt" -sh "RUNX1.dat"

efn2 - Elapsed time since the previous call: 0.51 seconds
efn2 - Current memory usage: 173.72 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/3f9e433f-405b-4406-a3ae-cdeb6fa1be0d/ct/RUNX1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/3f9e433f-405b-4406-a3ae-cdeb6fa1be0d/fold_dbn/RUNX1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 173.72 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'ACUCCACUGCCUUUAACCCUCAGCCUCAGAGUCAGAUGCAGGAUACAAGGCAGAUCCAACCAUCCCCACCGUGGUCCUA', '-structureDBN', '......(((((((....(((..((.((.......)).)))))....))))))).....(((((.......)))))....', '-o', '/disk1/www/rails/humanrnamap/public/result/3f9e433f-405b-4406-a3ae-cdeb6fa1be0d/final_image/RUNX1_fold_1.svg', '-title', 'RUNX1, -19.9 ± 0.8\n kcal/mol, AUC: 0.719', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,71,8,9,72,73,12,13,14,74,75,78,20,23,26,29,31,32,35,37,38,41,42,44,49,50,53,55,63', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '1,10,11,43,48,18,51,25,61,62', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '64,65,36,5,58,68,40,76,45,77,47,19,52,24,56', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '2,66,4,67,6,7,69,70,15,16,17,79,21,22,27,28,30,33,34,39,46,54,57,59,60']
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Text: 'A', X: 209.18186104487432, Y: 27.76417085330951, Width: 10.5, Height: 8
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Text: 'G', X: 224.78780953118343, Y: 35.682792215084135, Width: 10.5, Height: 8
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Text: 'U', X: 232.70643089295802, Y: 51.28874070139324, Width: 10.5, Height: 8
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Text: 'C', X: 229.88172106791865, Y: 68.5592707115814, Width: 10.5, Height: 8
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Text: 'G', X: 200.08825093886793, Y: 83.36332119596244, Width: 10.5, Height: 8
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Text: 'A', X: 142.25, Y: 150.64613817635052, Width: 10.5, Height: 8
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Text: 'G', X: 142.25, Y: 170.64613817635052, Width: 10.5, Height: 8
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Text: 'G', X: 142.25, Y: 190.64613817635052, Width: 10.5, Height: 8
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Text: 'A', X: 156.07308117397454, Y: 201.3779826147702, Width: 10.5, Height: 8
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Text: 'U', X: 163.76862412678466, Y: 217.09512856606113, Width: 10.5, Height: 8
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Text: 'A', X: 163.76862412678466, Y: 234.59513022871045, Width: 10.5, Height: 8
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Text: 'C', X: 156.07308117397457, Y: 250.3122761800015, Width: 10.5, Height: 8
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Text: 'A', X: 142.25, Y: 261.0441206184212, Width: 10.5, Height: 8
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Text: 'A', X: 142.25, Y: 281.0441206184212, Width: 10.5, Height: 8
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Text: 'G', X: 142.25, Y: 301.0441206184212, Width: 10.5, Height: 8
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Text: 'G', X: 142.25, Y: 321.0441206184212, Width: 10.5, Height: 8
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Text: 'C', X: 142.25, Y: 341.0441206184212, Width: 10.5, Height: 8
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Text: 'A', X: 142.25, Y: 361.0441206184212, Width: 10.5, Height: 8
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Text: 'G', X: 142.25, Y: 381.0441206184212, Width: 10.5, Height: 8
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Text: 'A', X: 159.75, Y: 381.0441206184212, Width: 10.5, Height: 8
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Text: 'U', X: 177.25, Y: 381.0441206184212, Width: 10.5, Height: 8
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Text: 'C', X: 194.75, Y: 381.0441206184212, Width: 10.5, Height: 8
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Text: 'C', X: 212.25, Y: 381.0441206184212, Width: 10.5, Height: 8
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Text: 'A', X: 229.75, Y: 381.0441206184212, Width: 10.5, Height: 8
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Text: 'A', X: 247.25, Y: 381.0441206184212, Width: 10.5, Height: 8
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Text: 'C', X: 247.25, Y: 361.0441206184212, Width: 10.5, Height: 8
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Text: 'C', X: 247.25, Y: 341.0441206184212, Width: 10.5, Height: 8
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Text: 'A', X: 247.25, Y: 321.0441206184212, Width: 10.5, Height: 8
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Text: 'U', X: 247.25, Y: 301.0441206184212, Width: 10.5, Height: 8
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Text: 'C', X: 236.79792334355562, Y: 287.0082990893372, Width: 10.5, Height: 8
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Text: 'C', X: 236.65087972320316, Y: 269.5089113685568, Width: 10.5, Height: 8
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Text: 'C', X: 246.86561713592346, Y: 255.2994310114973, Width: 10.5, Height: 8
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Text: 'C', X: 263.5, Y: 249.86366987253962, Width: 10.5, Height: 8
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Text: 'A', X: 280.13438286407654, Y: 255.2994310114973, Width: 10.5, Height: 8
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Text: 'C', X: 290.3491202767968, Y: 269.5089113685568, Width: 10.5, Height: 8
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Text: 'C', X: 290.2020766564444, Y: 287.0082990893372, Width: 10.5, Height: 8
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Text: 'G', X: 279.75, Y: 301.0441206184212, Width: 10.5, Height: 8
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Text: 'U', X: 279.75, Y: 321.0441206184212, Width: 10.5, Height: 8
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Text: 'G', X: 279.75, Y: 341.0441206184212, Width: 10.5, Height: 8
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Text: 'G', X: 279.75, Y: 361.0441206184212, Width: 10.5, Height: 8
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Text: 'U', X: 279.75, Y: 381.0441206184212, Width: 10.5, Height: 8
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Text: 'C', X: 297.25, Y: 381.0441206184212, Width: 10.5, Height: 8
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Text: 'C', X: 314.75, Y: 381.0441206184212, Width: 10.5, Height: 8
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Text: 'U', X: 332.25, Y: 381.0441206184212, Width: 10.5, Height: 8
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Text: 'A', X: 349.75, Y: 381.0441206184212, Width: 10.5, Height: 8
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Text: '1', X: 5.5, Y: 401.0441206184212, Width: 9.0, Height: 8
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Text: '10', X: 86.0, Y: 321.0441206184212, Width: 18.0, Height: 8
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Text: '20', X: 86.00000146490457, Y: 150.63848336213107, Width: 18.0, Height: 8
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Text: '30', X: 208.49413968686463, Y: 8.0, Width: 18.0, Height: 8
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Text: '40', X: 158.5, Y: 150.64613817635052, Width: 18.0, Height: 8
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Text: '50', X: 158.5, Y: 321.0441206184212, Width: 18.0, Height: 8
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Text: '60', X: 223.5, Y: 361.0441206184211, Width: 18.0, Height: 8
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Text: '70', X: 305.40992409060885, Y: 293.38011363960015, Width: 18.0, Height: 8
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Text: '79', X: 346.0, Y: 401.0441206184212, Width: 18.0, Height: 8
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Text: 'RUNX1, -19.9 ± 0.8
 kcal/mol, AUC: 0.719', X: 111.25, Y: 413.8441206184212, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 364.0, 413.8441206184212)
Updated viewBox: -0.25 -5.0 369.25 423.8441206184212
Updated SVG: /disk1/www/rails/humanrnamap/public/result/3f9e433f-405b-4406-a3ae-cdeb6fa1be0d/final_image/RUNX1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/3f9e433f-405b-4406-a3ae-cdeb6fa1be0d/final_image/RUNX1_fold_final_1.svg
