Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 97% [================================================= ] -                     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/c12c351a-ef2e-4ce8-aabc-5af0bae5f173/final_image/HCFC1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 156.30 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 156.30 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 156.30 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 169.93 MB
Based on canonical annotations, the following gene is in your area of interest: HCFC1(-)
write fasta - Elapsed time since the previous call: 0.25 seconds
write fasta - Current memory usage: 169.93 MB
Length of region: 87 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: 176.04 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/c12c351a-ef2e-4ce8-aabc-5af0bae5f173/fasta/HCFC1.fasta" "/disk1/www/rails/humanrnamap/public/result/c12c351a-ef2e-4ce8-aabc-5af0bae5f173/ct/HCFC1.ct" --SHAPE "HCFC1.dat"

fold - Elapsed time since the previous call: 0.12 seconds
fold - Current memory usage: 176.04 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/c12c351a-ef2e-4ce8-aabc-5af0bae5f173/ct/HCFC1.ct" "/disk1/www/rails/humanrnamap/public/result/c12c351a-ef2e-4ce8-aabc-5af0bae5f173/fold_FE/HCFC1.txt" -sh "HCFC1.dat"

efn2 - Elapsed time since the previous call: 0.45 seconds
efn2 - Current memory usage: 176.04 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/c12c351a-ef2e-4ce8-aabc-5af0bae5f173/ct/HCFC1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/c12c351a-ef2e-4ce8-aabc-5af0bae5f173/fold_dbn/HCFC1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 176.04 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AGCUUACACAUUUUCUCAGAGGCCUUUGUGCUCCCACCUCUUCUACCCUCCCCCUCUUCUUUCCCAUUUUAAAAAAGAAAAGAAGGA', '-structureDBN', '.................(((((..............))))).......(((..((.((((((...........)))))).))..)))', '-o', '/disk1/www/rails/humanrnamap/public/result/c12c351a-ef2e-4ce8-aabc-5af0bae5f173/final_image/HCFC1_fold_1.svg', '-title', 'HCFC1, -5.3 ± 0.9\n kcal/mol, AUC: 0.469', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,4,5,11,12,13,14,16,19,21,22,25,26,27,28,29,30,32,39,41,42,44,49,55,57,58,60,61,62,67,68,69,70,77,82,85,86', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '64,34,71,72,76,46,47,80,51,87,23,63', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,33,65,6,15,79,81,18,52,24,31', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '66,3,7,8,9,10,73,74,75,78,17,83,20,84,35,36,37,38,40,43,45,48,50,53,54,56,59']
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Text: 'A', X: 513.9283771514893, Y: 203.72051715427892, Width: 10.5, Height: 8
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Text: 'A', X: 507.25, Y: 219.8960535843617, Width: 10.5, Height: 8
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Text: 'G', X: 507.25, Y: 239.89605358436168, Width: 10.5, Height: 8
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Text: 'G', X: 507.25, Y: 285.5749355504948, Width: 10.5, Height: 8
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Text: 'G', X: 507.25, Y: 305.5749355504948, Width: 10.5, Height: 8
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Text: '10', X: 158.5, Y: 345.57493555049473, Width: 18.0, Height: 8
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Text: '20', X: 278.5, Y: 285.5749355504948, Width: 18.0, Height: 8
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Text: '30', X: 327.1997629847272, Y: 135.0148648315393, Width: 18.0, Height: 8
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Text: '40', X: 351.0, Y: 305.5749355504948, Width: 18.0, Height: 8
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Text: '50', X: 451.0, Y: 305.5749355504948, Width: 18.0, Height: 8
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Text: '80', X: 530.1783771514893, Y: 203.72051715427892, Width: 18.0, Height: 8
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Text: '87', X: 503.5, Y: 345.5749355504948, Width: 18.0, Height: 8
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Text: 'HCFC1, -5.3 ± 0.9
 kcal/mol, AUC: 0.469', X: 200.948896840923, Y: 358.3749355504948, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 551.6509318780603, 358.3749355504948)
Updated viewBox: -0.25 0.0 556.9009318780603 363.3749355504948
Updated SVG: /disk1/www/rails/humanrnamap/public/result/c12c351a-ef2e-4ce8-aabc-5af0bae5f173/final_image/HCFC1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/c12c351a-ef2e-4ce8-aabc-5af0bae5f173/final_image/HCFC1_fold_final_1.svg
