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/143dae4a-5e09-4708-9353-528798456d3c/final_image/FOXRED2_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.95 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.95 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.95 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.66 MB
Based on canonical annotations, the following gene is in your area of interest: FOXRED2(-)
write fasta - Elapsed time since the previous call: 0.32 seconds
write fasta - Current memory usage: 172.66 MB
Length of region: 86 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: 0.19 seconds
write dat - Current memory usage: 176.23 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/143dae4a-5e09-4708-9353-528798456d3c/fasta/FOXRED2.fasta" "/disk1/www/rails/humanrnamap/public/result/143dae4a-5e09-4708-9353-528798456d3c/ct/FOXRED2.ct" --SHAPE "FOXRED2.dat"

fold - Elapsed time since the previous call: 0.09 seconds
fold - Current memory usage: 176.23 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/143dae4a-5e09-4708-9353-528798456d3c/ct/FOXRED2.ct" "/disk1/www/rails/humanrnamap/public/result/143dae4a-5e09-4708-9353-528798456d3c/fold_FE/FOXRED2.txt" -sh "FOXRED2.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 176.23 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/143dae4a-5e09-4708-9353-528798456d3c/ct/FOXRED2.ct" 1 "/disk1/www/rails/humanrnamap/public/result/143dae4a-5e09-4708-9353-528798456d3c/fold_dbn/FOXRED2_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 176.23 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CACUGAGAAGCAGGAUUCAGAGCUGCUCUCCCCAGUUGCACCCCCUGACUCAUCUUCCAGCUGGCUCUUCUCUCCCAUCCUACUCC', '-structureDBN', '....((((.((((.........)))))))).(((((((...................)))))))......................', '-o', '/disk1/www/rails/humanrnamap/public/result/143dae4a-5e09-4708-9353-528798456d3c/final_image/FOXRED2_fold_1.svg', '-title', 'FOXRED2, -19.0 ± 0.8\n kcal/mol, AUC: 0.599', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '4,5,7,10,13,14,16,17,20,22,24,25,27,29,35,36,37,38,46,47,50,53,55,56,60,62,63,64,66,68,69,71,73,78,81,84', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '41,42,11,12,43,44,74,79,80,85,23,28', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '65,6,70,8,75,77,21,86,26,31,39,40,45,51,57,58,61', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,2,3,67,72,9,76,15,18,19,82,83,30,32,33,34,48,49,52,54,59']
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Text: 'FOXRED2, -19.0 ± 0.8
 kcal/mol, AUC: 0.599', X: 215.5, Y: 287.8389567286347, Width: 144.0, Height: 23
Calculated bounding box: (4.75, 0.0, 574.0, 287.8389567286347)
Updated viewBox: -0.25 -5.0 579.25 297.8389567286347
Updated SVG: /disk1/www/rails/humanrnamap/public/result/143dae4a-5e09-4708-9353-528798456d3c/final_image/FOXRED2_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/143dae4a-5e09-4708-9353-528798456d3c/final_image/FOXRED2_fold_final_1.svg
