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/c68bb44e-ace5-4633-8a79-92f1070a9a78/final_image/FOXRED2_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.84 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.84 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.84 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.40 MB
Based on canonical annotations, the following gene is in your area of interest: FOXRED2(-)
write fasta - Elapsed time since the previous call: 0.29 seconds
write fasta - Current memory usage: 172.40 MB
Length of region: 96 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: 176.11 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/c68bb44e-ace5-4633-8a79-92f1070a9a78/fasta/FOXRED2.fasta" "/disk1/www/rails/humanrnamap/public/result/c68bb44e-ace5-4633-8a79-92f1070a9a78/ct/FOXRED2.ct" --SHAPE "FOXRED2.dat"

fold - Elapsed time since the previous call: 0.12 seconds
fold - Current memory usage: 176.11 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/c68bb44e-ace5-4633-8a79-92f1070a9a78/ct/FOXRED2.ct" "/disk1/www/rails/humanrnamap/public/result/c68bb44e-ace5-4633-8a79-92f1070a9a78/fold_FE/FOXRED2.txt" -sh "FOXRED2.dat"

efn2 - Elapsed time since the previous call: 0.43 seconds
efn2 - Current memory usage: 176.11 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/c68bb44e-ace5-4633-8a79-92f1070a9a78/ct/FOXRED2.ct" 1 "/disk1/www/rails/humanrnamap/public/result/c68bb44e-ace5-4633-8a79-92f1070a9a78/fold_dbn/FOXRED2_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.11 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CCCGGCUGCUCUUCAGACACUACUCGCGUGCCUACUUCCCCGACGCCCGCGACAUGGUGCGCUACCUGGGUGACUUCGCGGACACGCUGGGGCUCC', '-structureDBN', '...((((((................))).))).....(((((.((.((((((...(((.((((.....)))))))))))))...)).)))))....', '-o', '/disk1/www/rails/humanrnamap/public/result/c68bb44e-ace5-4633-8a79-92f1070a9a78/final_image/FOXRED2_fold_1.svg', '-title', 'FOXRED2, -28.8 ± 1.1\n kcal/mol, AUC: 0.581', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '4,5,7,8,10,12,13,16,21,24,26,28,29,30,33,36,37,42,45,49,51,55,56,57,58,59,61,63,67,68,69,70,71,72,75,76,78,80,81,86,88,89,90,91,92,94', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '32,39,46,47,82,83,84,85,25,93,95', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,65,6,73,79,17,19,87,27,31,96,38,40,41,48,50,52,54,62', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,2,3,66,9,74,11,77,14,15,18,20,22,23,34,35,43,44,53,60']
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Text: 'FOXRED2, -28.8 ± 1.1
 kcal/mol, AUC: 0.581', X: 98.16021217228774, Y: 467.2258072344987, Width: 144.0, Height: 23
Calculated bounding box: (4.75, 5.0, 339.3204243445755, 467.2258072344987)
Updated viewBox: -0.25 0.0 344.5704243445755 472.2258072344987
Updated SVG: /disk1/www/rails/humanrnamap/public/result/c68bb44e-ace5-4633-8a79-92f1070a9a78/final_image/FOXRED2_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/c68bb44e-ace5-4633-8a79-92f1070a9a78/final_image/FOXRED2_fold_final_1.svg
