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/2b712bff-f3f4-4f77-a145-c5f33f258d99/final_image/ITCH_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 157.10 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 157.10 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 157.10 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 170.62 MB
Based on canonical annotations, the following gene is in your area of interest: ITCH(+)
write fasta - Elapsed time since the previous call: 0.29 seconds
write fasta - Current memory usage: 170.62 MB
Length of region: 99 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: 174.04 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/2b712bff-f3f4-4f77-a145-c5f33f258d99/fasta/ITCH.fasta" "/disk1/www/rails/humanrnamap/public/result/2b712bff-f3f4-4f77-a145-c5f33f258d99/ct/ITCH.ct" --SHAPE "ITCH.dat"

fold - Elapsed time since the previous call: 0.14 seconds
fold - Current memory usage: 174.04 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/2b712bff-f3f4-4f77-a145-c5f33f258d99/ct/ITCH.ct" "/disk1/www/rails/humanrnamap/public/result/2b712bff-f3f4-4f77-a145-c5f33f258d99/fold_FE/ITCH.txt" -sh "ITCH.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 174.04 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/2b712bff-f3f4-4f77-a145-c5f33f258d99/ct/ITCH.ct" 1 "/disk1/www/rails/humanrnamap/public/result/2b712bff-f3f4-4f77-a145-c5f33f258d99/fold_dbn/ITCH_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.04 seconds
ct2dot - Current memory usage: 174.04 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CUAGUCCAAAUAGAGGUCAGUGAAACAGCUUUUGACAUCAGAUUUUCAUUUGAGAGGGAGAGCUGUGGUACUGGCUAAAAAGAAAGGAAGAUAACAUCC', '-structureDBN', '(((.......))).((((((((..(((((((((....(((((......)))))....)))))))))..)))))))).........(((........)))', '-o', '/disk1/www/rails/humanrnamap/public/result/2b712bff-f3f4-4f77-a145-c5f33f258d99/final_image/ITCH_fold_1.svg', '-title', 'ITCH, -31.1 ± 1.3\n kcal/mol, AUC: 0.815', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,4,5,11,13,15,16,17,20,21,22,28,30,31,32,33,34,38,41,43,44,45,46,49,50,51,52,54,56,57,58,60,62,64,65,66,67,68,69,72,73,74,76,82,86,87,90,92,97', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '1,98,3,99,70,6,71,77,63', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '35,39,8,12,79,18,19,61,53,55,88,25,26,27,29', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '7,9,10,75,14,78,80,81,83,84,85,23,24,89,91,93,94,95,96,36,37,40,42,47,48,59']
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Text: 'G', X: 82.84912027679681, Y: 307.0213421063256, Width: 10.5, Height: 8
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Text: 'C', X: 82.84912027679681, Y: 287.0213421063256, Width: 10.5, Height: 8
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Text: 'U', X: 82.84912027679681, Y: 267.0213421063256, Width: 10.5, Height: 8
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Text: 'C', X: 82.84912027679681, Y: 116.62335966425496, Width: 10.5, Height: 8
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Text: 'A', X: 82.84912027679681, Y: 96.62335966425496, Width: 10.5, Height: 8
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Text: 'A', X: 82.84912027679681, Y: 56.62335966425496, Width: 10.5, Height: 8
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Text: 'U', X: 115.34912027679681, Y: 76.62335966425496, Width: 10.5, Height: 8
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Text: 'U', X: 115.34912027679681, Y: 96.62335966425496, Width: 10.5, Height: 8
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Text: 'A', X: 115.34912027679681, Y: 136.62335966425496, Width: 10.5, Height: 8
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Text: 'G', X: 115.34912027679681, Y: 207.02134210632562, Width: 10.5, Height: 8
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Text: 'A', X: 115.34912027679681, Y: 227.02134210632562, Width: 10.5, Height: 8
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Text: 'A', X: 115.34912027679681, Y: 267.0213421063256, Width: 10.5, Height: 8
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Text: 'G', X: 115.34912027679681, Y: 287.0213421063256, Width: 10.5, Height: 8
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Text: 'C', X: 115.34912027679681, Y: 307.0213421063256, Width: 10.5, Height: 8
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Text: 'U', X: 115.34912027679681, Y: 327.0213421063256, Width: 10.5, Height: 8
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Text: 'G', X: 115.34912027679681, Y: 347.0213421063256, Width: 10.5, Height: 8
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Text: 'U', X: 115.34912027679681, Y: 367.0213421063256, Width: 10.5, Height: 8
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Text: 'G', X: 125.72880359419858, Y: 381.1107813274567, Width: 10.5, Height: 8
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Text: 'C', X: 115.34912027679681, Y: 452.7002240724587, Width: 10.5, Height: 8
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Text: 'U', X: 115.34912027679681, Y: 472.7002240724587, Width: 10.5, Height: 8
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Text: 'G', X: 115.34912027679681, Y: 492.7002240724587, Width: 10.5, Height: 8
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Text: 'G', X: 115.34912027679681, Y: 512.7002240724587, Width: 10.5, Height: 8
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Text: 'C', X: 115.34912027679681, Y: 532.7002240724587, Width: 10.5, Height: 8
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Text: 'U', X: 115.34912027679681, Y: 552.7002240724587, Width: 10.5, Height: 8
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Text: 'A', X: 255.34912027679684, Y: 552.7002240724587, Width: 10.5, Height: 8
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Text: 'G', X: 290.34912027679684, Y: 552.7002240724587, Width: 10.5, Height: 8
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Text: 'G', X: 290.34912027679684, Y: 532.7002240724587, Width: 10.5, Height: 8
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Text: 'A', X: 330.0358748835015, Y: 466.38093625191283, Width: 10.5, Height: 8
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Text: 'U', X: 322.84912027679684, Y: 512.7002240724587, Width: 10.5, Height: 8
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Text: 'C', X: 322.84912027679684, Y: 532.7002240724587, Width: 10.5, Height: 8
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Text: 'C', X: 322.84912027679684, Y: 552.7002240724587, Width: 10.5, Height: 8
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Text: '30', X: 59.09912027679681, Y: 267.0213421063256, Width: 18.0, Height: 8
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Text: '40', X: 59.09912027679681, Y: 96.62335966425496, Width: 18.0, Height: 8
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Text: '50', X: 131.5991202767968, Y: 76.62335966425496, Width: 18.0, Height: 8
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Text: '60', X: 131.5991202767968, Y: 247.02134210632562, Width: 18.0, Height: 8
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Text: '70', X: 131.5991202767968, Y: 432.7002240724587, Width: 18.0, Height: 8
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Text: '80', X: 181.5991202767968, Y: 572.7002240724587, Width: 18.0, Height: 8
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Text: '90', X: 252.4389336699557, Y: 479.69044295817525, Width: 18.0, Height: 8
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Text: '99', X: 319.09912027679684, Y: 572.7002240724587, Width: 18.0, Height: 8
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Text: 'ITCH, -31.1 ± 1.3
 kcal/mol, AUC: 0.815', X: 104.96866548367257, Y: 585.5002240724586, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 347.68733096734513, 585.5002240724586)
Updated viewBox: -0.25 0.0 352.93733096734513 590.5002240724586
Updated SVG: /disk1/www/rails/humanrnamap/public/result/2b712bff-f3f4-4f77-a145-c5f33f258d99/final_image/ITCH_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/2b712bff-f3f4-4f77-a145-c5f33f258d99/final_image/ITCH_fold_final_1.svg
