Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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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/5fbab12b-13ed-4a28-94bf-10ab81f0bbe5/final_image/HSP90AB1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.00 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.00 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.00 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.61 MB
Based on canonical annotations, the following gene is in your area of interest: HSP90AB1(+)
write fasta - Elapsed time since the previous call: 0.49 seconds
write fasta - Current memory usage: 172.61 MB
Length of region: 90 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: 0.17 seconds
write dat - Current memory usage: 175.99 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/5fbab12b-13ed-4a28-94bf-10ab81f0bbe5/fasta/HSP90AB1.fasta" "/disk1/www/rails/humanrnamap/public/result/5fbab12b-13ed-4a28-94bf-10ab81f0bbe5/ct/HSP90AB1.ct" --SHAPE "HSP90AB1.dat"

fold - Elapsed time since the previous call: 0.09 seconds
fold - Current memory usage: 175.99 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/5fbab12b-13ed-4a28-94bf-10ab81f0bbe5/ct/HSP90AB1.ct" "/disk1/www/rails/humanrnamap/public/result/5fbab12b-13ed-4a28-94bf-10ab81f0bbe5/fold_FE/HSP90AB1.txt" -sh "HSP90AB1.dat"

efn2 - Elapsed time since the previous call: 0.42 seconds
efn2 - Current memory usage: 175.99 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/5fbab12b-13ed-4a28-94bf-10ab81f0bbe5/ct/HSP90AB1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/5fbab12b-13ed-4a28-94bf-10ab81f0bbe5/fold_dbn/HSP90AB1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 175.99 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AAGAUAAAGAUGAUGAAGAAAAACCCAAGAUCGAAGAUGUGGGUUCAGAUGAGGAGGAUGACAGCGGUAAGGAUAAGAAGAAGAAAACUA', '-structureDBN', '.....................((((((..(((...))).)))))).............................................', '-o', '/disk1/www/rails/humanrnamap/public/result/5fbab12b-13ed-4a28-94bf-10ab81f0bbe5/final_image/HSP90AB1_fold_1.svg', '-title', 'HSP90AB1, -4.8 ± 0.5\n kcal/mol, AUC: 0.575', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,5,9,11,12,14,15,18,29,31,33,36,38,39,40,41,42,43,44,45,48,50,51,53,54,56,57,59,60,64,66,67,68,71,72,74,77,80,83,89', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '23', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '73,58,85', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,2,4,6,7,8,10,13,16,17,19,20,21,22,24,25,26,27,28,30,32,34,35,37,46,47,49,52,55,61,62,63,65,69,70,75,76,78,79,81,82,84,86,87,88,90']
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Text: 'A', X: 1052.25, Y: 212.8761102970536, Width: 10.5, Height: 8
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Text: 'G', X: 1069.75, Y: 212.8761102970536, Width: 10.5, Height: 8
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Text: 'A', X: 1192.25, Y: 212.8761102970536, Width: 10.5, Height: 8
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Text: '1', X: 5.5, Y: 232.87611029705351, Width: 9.0, Height: 8
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Text: '10', X: 158.5, Y: 232.87611029705354, Width: 18.0, Height: 8
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Text: '20', X: 333.5, Y: 232.87611029705354, Width: 18.0, Height: 8
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Text: '30', X: 358.1193087479928, Y: 60.838718193649896, Width: 18.0, Height: 8
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Text: '40', X: 420.9229876455946, Y: 114.6295535591768, Width: 18.0, Height: 8
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Text: '50', X: 488.5, Y: 232.87611029705357, Width: 18.0, Height: 8
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Text: '60', X: 663.5, Y: 232.87611029705357, Width: 18.0, Height: 8
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Text: '70', X: 838.5, Y: 232.87611029705357, Width: 18.0, Height: 8
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Text: '80', X: 1013.5, Y: 232.87611029705357, Width: 18.0, Height: 8
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Text: '90', X: 1188.5, Y: 232.8761102970536, Width: 18.0, Height: 8
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Text: 'HSP90AB1, -4.8 ± 0.5
 kcal/mol, AUC: 0.575', X: 531.75, Y: 245.6761102970536, Width: 144.0, Height: 23
Calculated bounding box: (4.75, 5.0, 1206.5, 245.6761102970536)
Updated viewBox: -0.25 0.0 1211.75 250.6761102970536
Updated SVG: /disk1/www/rails/humanrnamap/public/result/5fbab12b-13ed-4a28-94bf-10ab81f0bbe5/final_image/HSP90AB1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/5fbab12b-13ed-4a28-94bf-10ab81f0bbe5/final_image/HSP90AB1_fold_final_1.svg
