Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
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 94% [================================================  ] /                     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/12fa1777-eb0e-4228-b234-87f49cb84203/final_image/RUNX1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 157.89 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 157.89 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 157.89 MB
read annotations - Elapsed time since the previous call: 0.10 seconds
read annotations - Current memory usage: 171.46 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: 171.46 MB
Length of region: 85 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: 0.31 seconds
write dat - Current memory usage: 174.70 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/12fa1777-eb0e-4228-b234-87f49cb84203/fasta/RUNX1.fasta" "/disk1/www/rails/humanrnamap/public/result/12fa1777-eb0e-4228-b234-87f49cb84203/ct/RUNX1.ct" --SHAPE "RUNX1.dat"

fold - Elapsed time since the previous call: 0.12 seconds
fold - Current memory usage: 174.70 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/12fa1777-eb0e-4228-b234-87f49cb84203/ct/RUNX1.ct" "/disk1/www/rails/humanrnamap/public/result/12fa1777-eb0e-4228-b234-87f49cb84203/fold_FE/RUNX1.txt" -sh "RUNX1.dat"

efn2 - Elapsed time since the previous call: 0.43 seconds
efn2 - Current memory usage: 174.70 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/12fa1777-eb0e-4228-b234-87f49cb84203/ct/RUNX1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/12fa1777-eb0e-4228-b234-87f49cb84203/fold_dbn/RUNX1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 174.70 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AAGAGUGCGUGUUUGCAUGUGUGUGACUCUGCGGCUGCUCAACUCCCAACAAACCAGAGGACCAGCCACAAACUUAACCAACAUC', '-structureDBN', '.((((((((((....))))).....)))))..(((((.((..(((...........))))).)))))..................', '-o', '/disk1/www/rails/humanrnamap/public/result/12fa1777-eb0e-4228-b234-87f49cb84203/final_image/RUNX1_fold_1.svg', '-title', 'RUNX1, -18.1 ± 1.1\n kcal/mol, AUC: 0.771', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,5,6,7,9,10,11,12,13,14,15,18,19,20,21,22,23,24,25,28,30,31,33,34,36,37,39,44,57,59,60,65,74,75,84', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '64,66,67,29,45,63', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '32,35,76,46,47,17,51,83,85,26,27,61', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,2,4,8,16,38,40,41,42,43,48,49,50,52,53,54,55,56,58,62,68,69,70,71,72,73,77,78,79,80,81,82']
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Text: 'A', X: 242.72340006314153, Y: 217.14546039815866, Width: 10.5, Height: 8
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Text: 'C', X: 242.72340006314153, Y: 277.14546039815866, Width: 10.5, Height: 8
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Text: 'A', X: 295.2234000631415, Y: 277.14546039815866, Width: 10.5, Height: 8
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Text: 'U', X: 365.2234000631415, Y: 277.14546039815866, Width: 10.5, Height: 8
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Text: '40', X: 187.9899560857669, Y: 137.1548653843991, Width: 18.0, Height: 8
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Text: '50', X: 306.8680547195306, Y: 8.0, Width: 18.0, Height: 8
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Text: '70', X: 291.4734000631415, Y: 297.14546039815866, Width: 18.0, Height: 8
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Text: '80', X: 466.4734000631415, Y: 297.14546039815866, Width: 18.0, Height: 8
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Text: '85', X: 553.9734000631415, Y: 297.14546039815866, Width: 18.0, Height: 8
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Text: 'RUNX1, -18.1 ± 1.1
 kcal/mol, AUC: 0.771', X: 215.23670003157076, Y: 309.9454603981587, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 571.9734000631415, 309.9454603981587)
Updated viewBox: -0.25 -5.0 577.2234000631415 319.9454603981587
Updated SVG: /disk1/www/rails/humanrnamap/public/result/12fa1777-eb0e-4228-b234-87f49cb84203/final_image/RUNX1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/12fa1777-eb0e-4228-b234-87f49cb84203/final_image/RUNX1_fold_final_1.svg
