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/a9a7bfde-67f1-4781-b876-1f1831880837/final_image/RUNX1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.32 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.32 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.32 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 171.93 MB
Based on canonical annotations, the following gene is in your area of interest: RUNX1(-)
write fasta - Elapsed time since the previous call: 0.13 seconds
write fasta - Current memory usage: 171.93 MB
Length of region: 93 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: 175.37 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/a9a7bfde-67f1-4781-b876-1f1831880837/fasta/RUNX1.fasta" "/disk1/www/rails/humanrnamap/public/result/a9a7bfde-67f1-4781-b876-1f1831880837/ct/RUNX1.ct" --SHAPE "RUNX1.dat"

fold - Elapsed time since the previous call: 0.15 seconds
fold - Current memory usage: 175.37 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/a9a7bfde-67f1-4781-b876-1f1831880837/ct/RUNX1.ct" "/disk1/www/rails/humanrnamap/public/result/a9a7bfde-67f1-4781-b876-1f1831880837/fold_FE/RUNX1.txt" -sh "RUNX1.dat"

efn2 - Elapsed time since the previous call: 0.53 seconds
efn2 - Current memory usage: 175.37 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/a9a7bfde-67f1-4781-b876-1f1831880837/ct/RUNX1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/a9a7bfde-67f1-4781-b876-1f1831880837/fold_dbn/RUNX1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.37 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CAUGUCUGACCUGCAAAAAUGCUGGAGAAAAAUGAAGGAAAAAAUUAUGUUUUUCAGUUUAAUUCUGUUAACUGAAGAUAUUCCAACUCAAAA', '-structureDBN', '(((.(((..((.(((....))).)))))...)))..((((.......(((.((((((((..........))))))))))))))).........', '-o', '/disk1/www/rails/humanrnamap/public/result/a9a7bfde-67f1-4781-b876-1f1831880837/final_image/RUNX1_fold_1.svg', '-title', 'RUNX1, -19.0 ± 1.2\n kcal/mol, AUC: 0.627', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,4,5,7,8,12,13,20,21,23,24,25,27,33,34,37,38,45,46,48,49,50,51,52,53,54,57,58,59,60,63,64,66,67,68,69,73,74,77,79,81,82,88', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '2,6,39,40,9,42,71,44,14,15,17,19,55,56,28', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '70,72,41,11,75,76,16,61,84,85,90,91,92,29,30', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,65,10,78,80,18,83,22,86,87,89,26,93,31,32,35,36,43,47,62']
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Text: 'A', X: 138.75115853554894, Y: 207.7780594247924, Width: 10.5, Height: 8
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Text: 'U', X: 454.88559143017244, Y: 254.86301039574928, Width: 10.5, Height: 8
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Text: 'U', X: 455.7115846510485, Y: 272.3434808673236, Width: 10.5, Height: 8
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Text: 'C', X: 448.2639296766947, Y: 288.1795646032571, Width: 10.5, Height: 8
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Text: 'G', X: 416.9898665750344, Y: 301.43747415765705, Width: 10.5, Height: 8
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Text: 'U', X: 388.4412398565687, Y: 283.03054336708306, Width: 10.5, Height: 8
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Text: 'U', X: 329.51391924148425, Y: 240.61988464749356, Width: 10.5, Height: 8
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Text: 'G', X: 311.41551161090774, Y: 232.10826663224574, Width: 10.5, Height: 8
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Text: 'C', X: 184.10959853403997, Y: 278.6895065597374, Width: 10.5, Height: 8
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Text: '40', X: 128.84692951497314, Y: 224.89582727102976, Width: 18.0, Height: 8
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Text: '60', X: 406.25662861832336, Y: 209.87406089154823, Width: 18.0, Height: 8
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Text: '70', X: 366.43291405528544, Y: 280.7946126123757, Width: 18.0, Height: 8
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Text: '93', X: 337.85959853403995, Y: 298.6895065597374, Width: 18.0, Height: 8
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Text: 'RUNX1, -19.0 ± 1.2
 kcal/mol, AUC: 0.627', X: 168.38855477515398, Y: 319.23747415765706, Width: 142.5, Height: 23
Calculated bounding box: (-4.0, 5.0, 466.2115846510485, 319.23747415765706)
Updated viewBox: -9.0 0.0 480.2115846510485 324.23747415765706
Updated SVG: /disk1/www/rails/humanrnamap/public/result/a9a7bfde-67f1-4781-b876-1f1831880837/final_image/RUNX1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/a9a7bfde-67f1-4781-b876-1f1831880837/final_image/RUNX1_fold_final_1.svg
