Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 96% [================================================= ] -                     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/2fd35a2c-7a65-4b5a-876a-acbd8e61dfb9/final_image/CLOCK_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.38 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.38 MB
config complete - Elapsed time since the previous call: 0.01 seconds
config complete - Current memory usage: 159.38 MB
read annotations - Elapsed time since the previous call: 0.11 seconds
read annotations - Current memory usage: 172.97 MB
Based on canonical annotations, the following gene is in your area of interest: CLOCK(-)
write fasta - Elapsed time since the previous call: 0.46 seconds
write fasta - Current memory usage: 172.97 MB
Length of region: 88 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: 0.45 seconds
write dat - Current memory usage: 176.36 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/2fd35a2c-7a65-4b5a-876a-acbd8e61dfb9/fasta/CLOCK.fasta" "/disk1/www/rails/humanrnamap/public/result/2fd35a2c-7a65-4b5a-876a-acbd8e61dfb9/ct/CLOCK.ct" --SHAPE "CLOCK.dat"

fold - Elapsed time since the previous call: 0.19 seconds
fold - Current memory usage: 176.36 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/2fd35a2c-7a65-4b5a-876a-acbd8e61dfb9/ct/CLOCK.ct" "/disk1/www/rails/humanrnamap/public/result/2fd35a2c-7a65-4b5a-876a-acbd8e61dfb9/fold_FE/CLOCK.txt" -sh "CLOCK.dat"

efn2 - Elapsed time since the previous call: 1.14 seconds
efn2 - Current memory usage: 176.36 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/2fd35a2c-7a65-4b5a-876a-acbd8e61dfb9/ct/CLOCK.ct" 1 "/disk1/www/rails/humanrnamap/public/result/2fd35a2c-7a65-4b5a-876a-acbd8e61dfb9/fold_dbn/CLOCK_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.10 seconds
ct2dot - Current memory usage: 176.36 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CCAAGAUUCUGGGUCAGAUAAUCGUAUAAACACAGUCAGUCUCAAGGAAGCAUUGGAAAGGUUUGAUCACAGCCCAACCCCUUCUGCC', '-structureDBN', '((((..(((((((...(((...............)))...)))..))))...))))...(((.((....)))))..............', '-o', '/disk1/www/rails/humanrnamap/public/result/2fd35a2c-7a65-4b5a-876a-acbd8e61dfb9/final_image/CLOCK_fold_1.svg', '-title', 'CLOCK, -13.9 ± 0.9\n kcal/mol, AUC: 0.85', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '5,7,8,10,11,12,13,14,17,19,22,24,25,27,35,36,39,40,42,46,47,50,53,54,55,56,60,61,62,63,64,65,67,72,82,83,85,86', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '1,2,3,4,70,9,41,73,74,81,84,87,88', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '34,37,71,43,75,77,15,16,48,49,20,21,57', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '66,68,69,6,76,78,79,80,18,23,26,28,29,30,31,32,33,38,44,45,51,52,58,59']
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Text: 'G', X: 346.90045362348997, Y: 338.4652910070896, Width: 10.5, Height: 8
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Text: 'C', X: 379.40045362348997, Y: 358.4652910070896, Width: 10.5, Height: 8
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Text: 'C', X: 396.90045362348997, Y: 358.4652910070896, Width: 10.5, Height: 8
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Text: '60', X: 329.008317999759, Y: 372.60742663082056, Width: 18.0, Height: 8
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Text: 'CLOCK, -13.9 ± 0.9
 kcal/mol, AUC: 0.85', X: 253.07522681174498, Y: 391.2652910070897, Width: 133.5, Height: 23
Calculated bounding box: (4.75, 0.0, 638.65045362349, 391.2652910070897)
Updated viewBox: -0.25 -5.0 643.90045362349 401.2652910070897
Updated SVG: /disk1/www/rails/humanrnamap/public/result/2fd35a2c-7a65-4b5a-876a-acbd8e61dfb9/final_image/CLOCK_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/2fd35a2c-7a65-4b5a-876a-acbd8e61dfb9/final_image/CLOCK_fold_final_1.svg
