Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  6% [====                                              ] -                     
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 37% [===================                               ] \                     
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 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/5b13b0ca-aeda-400f-b3e2-fb6dde4cc332/final_image/TGOLN2_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.29 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.29 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.29 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.93 MB
Based on canonical annotations, the following gene is in your area of interest: TGOLN2(-)
write fasta - Elapsed time since the previous call: 0.80 seconds
write fasta - Current memory usage: 172.93 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: 176.36 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/5b13b0ca-aeda-400f-b3e2-fb6dde4cc332/fasta/TGOLN2.fasta" "/disk1/www/rails/humanrnamap/public/result/5b13b0ca-aeda-400f-b3e2-fb6dde4cc332/ct/TGOLN2.ct" --SHAPE "TGOLN2.dat"

fold - Elapsed time since the previous call: 0.09 seconds
fold - Current memory usage: 176.36 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/5b13b0ca-aeda-400f-b3e2-fb6dde4cc332/ct/TGOLN2.ct" "/disk1/www/rails/humanrnamap/public/result/5b13b0ca-aeda-400f-b3e2-fb6dde4cc332/fold_FE/TGOLN2.txt" -sh "TGOLN2.dat"

efn2 - Elapsed time since the previous call: 0.42 seconds
efn2 - Current memory usage: 176.36 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/5b13b0ca-aeda-400f-b3e2-fb6dde4cc332/ct/TGOLN2.ct" 1 "/disk1/www/rails/humanrnamap/public/result/5b13b0ca-aeda-400f-b3e2-fb6dde4cc332/fold_dbn/TGOLN2_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 176.36 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AAGUCGGGUGCGGAGGCAAAGACCCAAAAAGACAGCUCCAACAAGUCGGGUGCGGAGGCAAAGACCCAAAAAGGCAGCAC', '-structureDBN', '.....((((((....))....)))).........(((((........((((((....))....)))).....)).)))..', '-o', '/disk1/www/rails/humanrnamap/public/result/5b13b0ca-aeda-400f-b3e2-fb6dde4cc332/final_image/TGOLN2_fold_1.svg', '-title', 'TGOLN2, -13.5 ± 2.4\n kcal/mol, AUC: 0.786', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,4,6,7,8,9,10,73,12,13,74,15,16,77,21,31,35,37,45,46,48,49,50,51,52,54,55,57,58,63', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '26,68', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '64,65,66,67,70,24,25', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,2,5,11,14,17,18,19,20,22,23,27,28,29,30,32,33,34,36,38,39,40,41,42,43,44,47,53,56,59,60,61,62,69,71,72,75,76,78,79,80']
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Text: 'TGOLN2, -13.5 ± 2.4
 kcal/mol, AUC: 0.786', X: 120.0, Y: 348.8375183257322, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 381.5, 348.8375183257322)
Updated viewBox: -0.25 -5.0 386.75 358.8375183257322
Updated SVG: /disk1/www/rails/humanrnamap/public/result/5b13b0ca-aeda-400f-b3e2-fb6dde4cc332/final_image/TGOLN2_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/5b13b0ca-aeda-400f-b3e2-fb6dde4cc332/final_image/TGOLN2_fold_final_1.svg
