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/e478e3d5-6aa5-4115-b908-a5318b7ccea4/final_image/RUNX1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.18 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.18 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.18 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.73 MB
Based on canonical annotations, the following gene is in your area of interest: RUNX1(-)
write fasta - Elapsed time since the previous call: 0.14 seconds
write fasta - Current memory usage: 172.73 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: 0.21 seconds
write dat - Current memory usage: 176.09 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/e478e3d5-6aa5-4115-b908-a5318b7ccea4/fasta/RUNX1.fasta" "/disk1/www/rails/humanrnamap/public/result/e478e3d5-6aa5-4115-b908-a5318b7ccea4/ct/RUNX1.ct" --SHAPE "RUNX1.dat"

fold - Elapsed time since the previous call: 0.12 seconds
fold - Current memory usage: 176.09 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/e478e3d5-6aa5-4115-b908-a5318b7ccea4/ct/RUNX1.ct" "/disk1/www/rails/humanrnamap/public/result/e478e3d5-6aa5-4115-b908-a5318b7ccea4/fold_FE/RUNX1.txt" -sh "RUNX1.dat"

efn2 - Elapsed time since the previous call: 0.51 seconds
efn2 - Current memory usage: 176.09 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/e478e3d5-6aa5-4115-b908-a5318b7ccea4/ct/RUNX1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/e478e3d5-6aa5-4115-b908-a5318b7ccea4/fold_dbn/RUNX1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.09 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CACAUUGAAGAAGGCUAGAAAAAAAGAAUGAGUAAUGUGAUCGCUUGGUUAUCCAGAAGUAUUGUUUACAUUAAACUCCCUUUCAUGUUAAUCAAA', '-structureDBN', '(((((((.......((........))......))))))).....(((((((..((((((....(((((...)))))....)))).)).))))))).', '-o', '/disk1/www/rails/humanrnamap/public/result/e478e3d5-6aa5-4115-b908-a5318b7ccea4/final_image/RUNX1_fold_1.svg', '-title', 'RUNX1, -6.9 ± 1.0\n kcal/mol, AUC: 0.559', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '5,6,7,10,13,14,16,18,26,29,30,32,33,36,37,38,39,41,43,45,46,47,48,49,50,52,56,59,60,62,63,64,65,66,67,71,72,77,81,82,83,86,87,88,89,92', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '19,4,20,21,51,40,24', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '2,3,34,68,73,78,79,17,55,23,25,27,94', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,69,70,8,9,74,11,12,75,76,15,80,84,85,22,90,91,28,93,31,95,96,35,42,44,53,54,57,58,61']
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Text: 'U', X: 86.21657426553138, Y: 445.5016982859731, Width: 10.5, Height: 8
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Text: 'G', X: 156.21657426553136, Y: 465.5016982859731, Width: 10.5, Height: 8
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Text: 'C', X: 173.71657426553136, Y: 465.5016982859731, Width: 10.5, Height: 8
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Text: 'U', X: 191.21657426553136, Y: 465.5016982859731, Width: 10.5, Height: 8
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Text: 'U', X: 191.21657426553136, Y: 445.5016982859731, Width: 10.5, Height: 8
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Text: 'G', X: 191.21657426553136, Y: 425.5016982859731, Width: 10.5, Height: 8
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Text: 'G', X: 191.21657426553136, Y: 405.5016982859731, Width: 10.5, Height: 8
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Text: 'U', X: 191.21657426553136, Y: 385.5016982859731, Width: 10.5, Height: 8
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Text: 'U', X: 191.21657426553136, Y: 365.5016982859731, Width: 10.5, Height: 8
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Text: 'A', X: 191.21657426553136, Y: 345.5016982859731, Width: 10.5, Height: 8
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Text: 'G', X: 209.1605373776168, Y: 133.95182584542658, Width: 10.5, Height: 8
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Text: 'U', X: 209.1605373776168, Y: 113.95182584542658, Width: 10.5, Height: 8
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Text: 'A', X: 209.1605373776168, Y: 53.95182584542658, Width: 10.5, Height: 8
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Text: 'A', X: 241.6605373776168, Y: 93.95182584542658, Width: 10.5, Height: 8
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Text: 'A', X: 241.6605373776168, Y: 113.95182584542658, Width: 10.5, Height: 8
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Text: 'C', X: 241.6605373776168, Y: 133.95182584542658, Width: 10.5, Height: 8
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Text: 'A', X: 241.21657426553136, Y: 465.5016982859731, Width: 10.5, Height: 8
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Text: '40', X: 99.96657426553138, Y: 485.5016982859731, Width: 18.0, Height: 8
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Text: '50', X: 167.46657426553136, Y: 365.5016982859731, Width: 18.0, Height: 8
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Text: '90', X: 239.96657426553136, Y: 365.5016982859731, Width: 18.0, Height: 8
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Text: '96', X: 237.46657426553136, Y: 485.5016982859731, Width: 18.0, Height: 8
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Text: 'RUNX1, -6.9 ± 1.0
 kcal/mol, AUC: 0.559', X: 74.4188538021568, Y: 498.3016982859731, Width: 142.5, Height: 23
Calculated bounding box: (-4.0, 0.0, 285.2476219926023, 498.3016982859731)
Updated viewBox: -9.0 -5.0 299.2476219926023 508.3016982859731
Updated SVG: /disk1/www/rails/humanrnamap/public/result/e478e3d5-6aa5-4115-b908-a5318b7ccea4/final_image/RUNX1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/e478e3d5-6aa5-4115-b908-a5318b7ccea4/final_image/RUNX1_fold_final_1.svg
