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/009b0cac-c5d7-4aa4-b6c8-aa6978e7877f/final_image/HTT_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.30 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.30 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.30 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 171.91 MB
Based on canonical annotations, the following gene is in your area of interest: HTT(+)
write fasta - Elapsed time since the previous call: 0.35 seconds
write fasta - Current memory usage: 171.91 MB
Length of region: 85 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: 0.18 seconds
write dat - Current memory usage: 175.47 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/009b0cac-c5d7-4aa4-b6c8-aa6978e7877f/fasta/HTT.fasta" "/disk1/www/rails/humanrnamap/public/result/009b0cac-c5d7-4aa4-b6c8-aa6978e7877f/ct/HTT.ct" --SHAPE "HTT.dat"

fold - Elapsed time since the previous call: 0.10 seconds
fold - Current memory usage: 175.47 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/009b0cac-c5d7-4aa4-b6c8-aa6978e7877f/ct/HTT.ct" "/disk1/www/rails/humanrnamap/public/result/009b0cac-c5d7-4aa4-b6c8-aa6978e7877f/fold_FE/HTT.txt" -sh "HTT.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 175.47 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/009b0cac-c5d7-4aa4-b6c8-aa6978e7877f/ct/HTT.ct" 1 "/disk1/www/rails/humanrnamap/public/result/009b0cac-c5d7-4aa4-b6c8-aa6978e7877f/fold_dbn/HTT_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.47 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CAGGUCAGCGCCGUCCCAUCUGACCCUGCCAUGGACCUGAAUGAUGGGACCCAGGCCUCGUCGCCCAUCAGCGACAGCUCCCAGA', '-structureDBN', '.(((((......((((((((....((......))........))))))))...))))).(((((......)))))..........', '-o', '/disk1/www/rails/humanrnamap/public/result/009b0cac-c5d7-4aa4-b6c8-aa6978e7877f/final_image/HTT_fold_1.svg', '-title', 'HTT, -32.8 ± 1.2\n kcal/mol, AUC: 0.93', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,4,5,8,10,13,14,19,21,22,27,28,32,33,34,38,39,42,43,45,46,47,48,54,55,58,60,61,63,68,71,73,77,79,84', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '64,6,72,74,75,15,16,49,20,53,56,57,62', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,2,36,37,70,11,44,17,18,50,52,24,25,26,31', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '65,66,67,69,7,9,12,76,78,80,81,82,83,85,23,29,30,35,40,41,51,59']
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Text: 'G', X: 225.43858203585683, Y: 90.40989758732655, Width: 10.5, Height: 8
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Text: 'G', X: 250.9564433756559, Y: 164.41713964607447, Width: 10.5, Height: 8
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Text: 'A', X: 238.6723736489741, Y: 177.4699413862735, Width: 10.5, Height: 8
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Text: 'A', X: 222.55895122929047, Y: 185.32052227202706, Width: 10.5, Height: 8
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Text: 'U', X: 204.7089862390602, Y: 186.94924943348707, Width: 10.5, Height: 8
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Text: 'G', X: 187.44083082248025, Y: 182.1445839063391, Width: 10.5, Height: 8
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Text: 'A', X: 173.2986951987493, Y: 196.28671953007003, Width: 10.5, Height: 8
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Text: 'U', X: 159.15655957501835, Y: 210.42885515380098, Width: 10.5, Height: 8
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Text: 'G', X: 145.0144239512874, Y: 224.57099077753193, Width: 10.5, Height: 8
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Text: 'G', X: 130.87228832755645, Y: 238.71312640126288, Width: 10.5, Height: 8
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Text: 'G', X: 116.73015270382548, Y: 252.85526202499383, Width: 10.5, Height: 8
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Text: 'A', X: 102.5880170800945, Y: 266.9973976487248, Width: 10.5, Height: 8
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Text: 'C', X: 88.44588145636354, Y: 281.13953327245565, Width: 10.5, Height: 8
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Text: 'C', X: 91.4528349839933, Y: 296.8498619752776, Width: 10.5, Height: 8
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Text: 'C', X: 88.2944310827227, Y: 312.53044494481276, Width: 10.5, Height: 8
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Text: 'A', X: 79.43991334832064, Y: 325.8516203118437, Width: 10.5, Height: 8
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Text: 'G', X: 66.2047961577858, Y: 334.8342630421789, Width: 10.5, Height: 8
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Text: 'G', X: 66.2047961577858, Y: 354.8342630421789, Width: 10.5, Height: 8
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Text: 'C', X: 66.2047961577858, Y: 374.8342630421789, Width: 10.5, Height: 8
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Text: 'C', X: 66.2047961577858, Y: 394.8342630421789, Width: 10.5, Height: 8
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Text: 'U', X: 66.2047961577858, Y: 414.8342630421789, Width: 10.5, Height: 8
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Text: 'C', X: 83.7047961577858, Y: 414.8342630421789, Width: 10.5, Height: 8
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Text: 'G', X: 101.2047961577858, Y: 414.8342630421789, Width: 10.5, Height: 8
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Text: 'U', X: 101.2047961577858, Y: 394.8342630421789, Width: 10.5, Height: 8
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Text: 'C', X: 101.2047961577858, Y: 374.8342630421789, Width: 10.5, Height: 8
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Text: 'G', X: 101.2047961577858, Y: 354.8342630421789, Width: 10.5, Height: 8
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Text: 'C', X: 101.2047961577858, Y: 334.8342630421789, Width: 10.5, Height: 8
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Text: 'C', X: 92.35789606628295, Y: 319.7352064295942, Width: 10.5, Height: 8
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Text: 'C', X: 95.3231011811789, Y: 302.48827306607507, Width: 10.5, Height: 8
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Text: 'A', X: 108.70480827466459, Y: 291.21090337792407, Width: 10.5, Height: 8
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Text: 'U', X: 126.20478404090701, Y: 291.21090337792407, Width: 10.5, Height: 8
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Text: 'C', X: 139.5864911343927, Y: 302.48827306607507, Width: 10.5, Height: 8
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Text: 'A', X: 142.55169624928865, Y: 319.7352064295942, Width: 10.5, Height: 8
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Text: 'G', X: 133.7047961577858, Y: 334.8342630421789, Width: 10.5, Height: 8
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Text: 'C', X: 133.7047961577858, Y: 354.8342630421789, Width: 10.5, Height: 8
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Text: 'G', X: 133.7047961577858, Y: 374.8342630421789, Width: 10.5, Height: 8
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Text: 'A', X: 133.7047961577858, Y: 394.8342630421789, Width: 10.5, Height: 8
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Text: 'C', X: 133.7047961577858, Y: 414.8342630421789, Width: 10.5, Height: 8
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Text: 'A', X: 151.2047961577858, Y: 414.8342630421789, Width: 10.5, Height: 8
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Text: 'G', X: 168.7047961577858, Y: 414.8342630421789, Width: 10.5, Height: 8
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Text: 'C', X: 186.2047961577858, Y: 414.8342630421789, Width: 10.5, Height: 8
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Text: 'U', X: 203.7047961577858, Y: 414.8342630421789, Width: 10.5, Height: 8
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Text: 'C', X: 221.2047961577858, Y: 414.8342630421789, Width: 10.5, Height: 8
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Text: 'C', X: 238.7047961577858, Y: 414.8342630421789, Width: 10.5, Height: 8
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Text: 'C', X: 256.2047961577858, Y: 414.834263042179, Width: 10.5, Height: 8
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Text: 'A', X: 273.7047961577858, Y: 414.834263042179, Width: 10.5, Height: 8
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Text: 'G', X: 291.2047961577858, Y: 414.834263042179, Width: 10.5, Height: 8
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Text: 'A', X: 308.7047961577858, Y: 414.834263042179, Width: 10.5, Height: 8
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Text: '1', X: 16.954796157785797, Y: 434.8342630421789, Width: 9.0, Height: 8
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Text: '10', X: -4.0, Y: 261.1313905262763, Width: 18.0, Height: 8
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Text: '20', X: 141.82475567076247, Y: 152.57932782495743, Width: 18.0, Height: 8
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Text: '30', X: 221.0490358554129, Y: 8.0, Width: 18.0, Height: 8
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Text: '40', X: 246.778601973711, Y: 193.5767675761753, Width: 18.0, Height: 8
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Text: '50', X: 103.15495534300966, Y: 288.8377532775828, Width: 18.0, Height: 8
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Text: '60', X: 83.31266053405484, Y: 428.97639866590987, Width: 18.0, Height: 8
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Text: '70', X: 158.4790295768004, Y: 323.3132719848901, Width: 18.0, Height: 8
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Text: '80', X: 217.4547961577858, Y: 434.8342630421789, Width: 18.0, Height: 8
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Text: '85', X: 304.9547961577858, Y: 434.834263042179, Width: 18.0, Height: 8
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Text: 'HTT, -32.8 ± 1.2
 kcal/mol, AUC: 0.93', X: 97.37851163845829, Y: 447.634263042179, Width: 133.5, Height: 23
Calculated bounding box: (-4.0, 0.0, 322.9547961577858, 447.634263042179)
Updated viewBox: -9.0 -5.0 336.9547961577858 457.634263042179
Updated SVG: /disk1/www/rails/humanrnamap/public/result/009b0cac-c5d7-4aa4-b6c8-aa6978e7877f/final_image/HTT_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/009b0cac-c5d7-4aa4-b6c8-aa6978e7877f/final_image/HTT_fold_final_1.svg
