Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 98% [==================================================] \                     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/d7ad0b7a-24ac-401d-80d9-98ba8eb18eca/final_image/ACLY_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.35 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.35 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.35 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 171.96 MB
Based on canonical annotations, the following gene is in your area of interest: ACLY(-)
write fasta - Elapsed time since the previous call: 0.57 seconds
write fasta - Current memory usage: 171.96 MB
Length of region: 71 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: 174.93 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/d7ad0b7a-24ac-401d-80d9-98ba8eb18eca/fasta/ACLY.fasta" "/disk1/www/rails/humanrnamap/public/result/d7ad0b7a-24ac-401d-80d9-98ba8eb18eca/ct/ACLY.ct" --SHAPE "ACLY.dat"

fold - Elapsed time since the previous call: 0.08 seconds
fold - Current memory usage: 174.93 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/d7ad0b7a-24ac-401d-80d9-98ba8eb18eca/ct/ACLY.ct" "/disk1/www/rails/humanrnamap/public/result/d7ad0b7a-24ac-401d-80d9-98ba8eb18eca/fold_FE/ACLY.txt" -sh "ACLY.dat"

efn2 - Elapsed time since the previous call: 0.40 seconds
efn2 - Current memory usage: 174.93 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/d7ad0b7a-24ac-401d-80d9-98ba8eb18eca/ct/ACLY.ct" 1 "/disk1/www/rails/humanrnamap/public/result/d7ad0b7a-24ac-401d-80d9-98ba8eb18eca/fold_dbn/ACLY_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 174.93 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CAGCCACUGGGGUACAGGCACCGAAGACCAACAUCCACAGGCUAACACCCCUUCAGUCCACACAAAGAAGC', '-structureDBN', '..((....(((((...(((......((......)).....)))...)))))....))..............', '-o', '/disk1/www/rails/humanrnamap/public/result/d7ad0b7a-24ac-401d-80d9-98ba8eb18eca/final_image/ACLY_fold_1.svg', '-title', 'ACLY, -12.7 ± 0.9\n kcal/mol, AUC: 0.883', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,67,70,8,9,10,11,12,13,17,18,23,26,34,40,41,43,52,53,56,57', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '4,48,49,50,19,51,60,29', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '32,33,64,35,36,5,66,71,59,47,55,58,27,31', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,2,65,68,69,6,7,14,15,16,20,21,22,24,25,28,30,37,38,39,42,44,45,46,54,61,62,63']
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Text: 'U', X: 72.25, Y: 447.9189610530117, Width: 10.5, Height: 8
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Text: 'ACLY, -12.7 ± 0.9
 kcal/mol, AUC: 0.883', X: 95.0, Y: 480.7189610530117, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 331.5, 480.7189610530117)
Updated viewBox: -0.25 -5.0 336.75 490.7189610530117
Updated SVG: /disk1/www/rails/humanrnamap/public/result/d7ad0b7a-24ac-401d-80d9-98ba8eb18eca/final_image/ACLY_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/d7ad0b7a-24ac-401d-80d9-98ba8eb18eca/final_image/ACLY_fold_final_1.svg
