Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 97% [================================================= ] -                     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/1712a355-a73e-44fe-848e-315c24981b49/final_image/NFKB1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.12 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.12 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.12 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.74 MB
Based on canonical annotations, the following gene is in your area of interest: NFKB1(+)
write fasta - Elapsed time since the previous call: 0.71 seconds
write fasta - Current memory usage: 172.74 MB
Length of region: 108 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: 0.24 seconds
write dat - Current memory usage: 176.24 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/1712a355-a73e-44fe-848e-315c24981b49/fasta/NFKB1.fasta" "/disk1/www/rails/humanrnamap/public/result/1712a355-a73e-44fe-848e-315c24981b49/ct/NFKB1.ct" --SHAPE "NFKB1.dat"

fold - Elapsed time since the previous call: 0.18 seconds
fold - Current memory usage: 176.24 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/1712a355-a73e-44fe-848e-315c24981b49/ct/NFKB1.ct" "/disk1/www/rails/humanrnamap/public/result/1712a355-a73e-44fe-848e-315c24981b49/fold_FE/NFKB1.txt" -sh "NFKB1.dat"

efn2 - Elapsed time since the previous call: 0.47 seconds
efn2 - Current memory usage: 176.24 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/1712a355-a73e-44fe-848e-315c24981b49/ct/NFKB1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/1712a355-a73e-44fe-848e-315c24981b49/fold_dbn/NFKB1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 176.24 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CGUGUAUAAGGGGCUAUAAUCCUGGACUCUUGGUGCACCCUGACCUUGCCUAUUUGCAAGCAGAAGGUGGAGGGGACCGGCAGCUGGGAGAUCGGGAAAAAGAGCUAA', '-structureDBN', '...........((((....((((((.((((((((((.((((..((..((((.((((....)))))))))).))))....)).)))))))).)))))).....))))..', '-o', '/disk1/www/rails/humanrnamap/public/result/1712a355-a73e-44fe-848e-315c24981b49/final_image/NFKB1_fold_1.svg', '-title', 'NFKB1, -34.2 ± 1.4\n kcal/mol, AUC: 0.747', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,4,5,7,10,11,12,13,15,17,20,23,24,25,28,30,31,32,33,34,35,41,42,46,47,48,51,53,54,55,56,60,63,66,67,68,69,70,72,73,74,75,79,80,83,85,86,87,88,90,92,94,95,96,102,104,106', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '97,99,38,40,9,105,14,22', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '77,16,84,21,89,26,91,27,29,98,36,39,103,45,49,58,59', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,1,65,6,71,8,76,78,81,18,19,82,93,100,37,101,43,44,107,108,50,52,57,61,62']
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Text: '70', X: 103.3710792351684, Y: 174.62414901754835, Width: 18.0, Height: 8
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Text: '108', X: 372.86844525988477, Y: 691.4214230359364, Width: 27.0, Height: 8
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Text: 'NFKB1, -34.2 ± 1.4
 kcal/mol, AUC: 0.747', X: 126.93422262994238, Y: 704.2214230359364, Width: 142.5, Height: 23
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Updated viewBox: -2.9954312025636725 0.0 417.76576405173194 709.2214230359364
Updated SVG: /disk1/www/rails/humanrnamap/public/result/1712a355-a73e-44fe-848e-315c24981b49/final_image/NFKB1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/1712a355-a73e-44fe-848e-315c24981b49/final_image/NFKB1_fold_final_1.svg
