Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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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/1a211931-81d4-4c8d-9524-dcf29734153f/final_image/NFKB1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.97 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.97 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.97 MB
read annotations - Elapsed time since the previous call: 0.14 seconds
read annotations - Current memory usage: 172.68 MB
Based on canonical annotations, the following gene is in your area of interest: NFKB1(+)
write fasta - Elapsed time since the previous call: 0.78 seconds
write fasta - Current memory usage: 172.68 MB
Length of region: 92 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: 0.23 seconds
write dat - Current memory usage: 176.24 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/1a211931-81d4-4c8d-9524-dcf29734153f/fasta/NFKB1.fasta" "/disk1/www/rails/humanrnamap/public/result/1a211931-81d4-4c8d-9524-dcf29734153f/ct/NFKB1.ct" --SHAPE "NFKB1.dat"

fold - Elapsed time since the previous call: 0.19 seconds
fold - Current memory usage: 176.24 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/1a211931-81d4-4c8d-9524-dcf29734153f/ct/NFKB1.ct" "/disk1/www/rails/humanrnamap/public/result/1a211931-81d4-4c8d-9524-dcf29734153f/fold_FE/NFKB1.txt" -sh "NFKB1.dat"

efn2 - Elapsed time since the previous call: 0.42 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/1a211931-81d4-4c8d-9524-dcf29734153f/ct/NFKB1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/1a211931-81d4-4c8d-9524-dcf29734153f/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', 'CCAUGGUGGACUACCUGGUGCCUCUAGUGAAAAGAACAAGAAGUCUUACCCUCAGGUCAAAAUCUGCAACUAUGUGGGACCAGCAAAGGUUA', '-structureDBN', '(((.((((...))))))).((((....((.............(((((((...(((((....))))).......)))))))))....))))..', '-o', '/disk1/www/rails/humanrnamap/public/result/1a211931-81d4-4c8d-9524-dcf29734153f/final_image/NFKB1_fold_1.svg', '-title', 'NFKB1, -18.6 ± 1.3\n kcal/mol, AUC: 0.74', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '4,5,6,7,8,9,12,16,17,18,19,20,23,25,27,28,29,34,40,43,44,46,47,52,55,56,57,63,65,66,71,73,74,75,76,77,78,83,88,89,90,91', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '2,15,48,79,50,81,82,21,22,84,58,60,62', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '72,41,45,14,51,53,54,24,92,61,30', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,1,3,67,68,69,70,10,11,13,80,85,86,87,26,31,32,33,35,36,37,38,39,42,49,59']
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Text: 'A', X: 274.105166632588, Y: 228.64323947198915, Width: 10.5, Height: 8
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Text: 'U', X: 222.1327461546467, Y: 192.59914272311488, Width: 10.5, Height: 8
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Text: 'G', X: 222.67714215739926, Y: 175.10761240149384, Width: 10.5, Height: 8
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Text: 'U', X: 206.24263232239923, Y: 163.70994217976482, Width: 10.5, Height: 8
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Text: 'G', X: 189.8081224873992, Y: 152.31227195803584, Width: 10.5, Height: 8
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Text: 'A', X: 143.56561886658267, Y: 265.2350887380477, Width: 10.5, Height: 8
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Text: '20', X: 58.17348324285172, Y: 279.37722436177864, Width: 18.0, Height: 8
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Text: '40', X: 143.38824814135404, Y: 17.494206515239284, Width: 18.0, Height: 8
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Text: '50', X: 249.86122467501843, Y: 122.12165262238071, Width: 18.0, Height: 8
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Text: '60', X: 432.1283798162855, Y: 170.12555100558285, Width: 18.0, Height: 8
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Text: '70', X: 248.72290393707738, Y: 248.05334573819687, Width: 18.0, Height: 8
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Text: '80', X: 132.41887684154477, Y: 122.64701700408955, Width: 18.0, Height: 8
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Text: '90', X: 118.95775449031362, Y: 279.37722436177864, Width: 18.0, Height: 8
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Text: '92', X: 139.81561886658267, Y: 285.2350887380477, Width: 18.0, Height: 8
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Text: 'NFKB1, -18.6 ± 1.3
 kcal/mol, AUC: 0.74', X: 149.13424197140887, Y: 298.0350887380477, Width: 133.5, Height: 23
Calculated bounding box: (4.75, 5.0, 450.1283798162855, 298.0350887380477)
Updated viewBox: -0.25 0.0 455.3783798162855 303.0350887380477
Updated SVG: /disk1/www/rails/humanrnamap/public/result/1a211931-81d4-4c8d-9524-dcf29734153f/final_image/NFKB1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/1a211931-81d4-4c8d-9524-dcf29734153f/final_image/NFKB1_fold_final_1.svg
