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/268d3893-0510-4fc4-8ac8-bf21a6dec77d/final_image/CLOCK_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 154.87 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 154.87 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 154.87 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 168.34 MB
Based on canonical annotations, the following gene is in your area of interest: CLOCK(-)
write fasta - Elapsed time since the previous call: 0.32 seconds
write fasta - Current memory usage: 168.34 MB
Length of region: 95 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: 0.19 seconds
write dat - Current memory usage: 171.46 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/268d3893-0510-4fc4-8ac8-bf21a6dec77d/fasta/CLOCK.fasta" "/disk1/www/rails/humanrnamap/public/result/268d3893-0510-4fc4-8ac8-bf21a6dec77d/ct/CLOCK.ct" --SHAPE "CLOCK.dat"

fold - Elapsed time since the previous call: 0.12 seconds
fold - Current memory usage: 171.46 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/268d3893-0510-4fc4-8ac8-bf21a6dec77d/ct/CLOCK.ct" "/disk1/www/rails/humanrnamap/public/result/268d3893-0510-4fc4-8ac8-bf21a6dec77d/fold_FE/CLOCK.txt" -sh "CLOCK.dat"

efn2 - Elapsed time since the previous call: 0.50 seconds
efn2 - Current memory usage: 171.46 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/268d3893-0510-4fc4-8ac8-bf21a6dec77d/ct/CLOCK.ct" 1 "/disk1/www/rails/humanrnamap/public/result/268d3893-0510-4fc4-8ac8-bf21a6dec77d/fold_dbn/CLOCK_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 171.46 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AGGCAAAGAUUUAAUUGAAAUCCAAAAUGAUUUAUAGAAACGAAAGGCAUUUUCCAUUUGUUGUCUUCUGCCGAAAUUCUGAAUUGCAUACACAC', '-structureDBN', '.((((((((........(((((......))))).....((((((.((......)).)))))).)))).)))).......................', '-o', '/disk1/www/rails/humanrnamap/public/result/268d3893-0510-4fc4-8ac8-bf21a6dec77d/final_image/CLOCK_fold_1.svg', '-title', 'CLOCK, -9.7 ± 0.6\n kcal/mol, AUC: 0.595', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,8,10,11,12,15,16,17,21,28,29,31,32,33,35,37,42,46,47,50,51,52,53,57,58,59,60,61,62,63,64,66,67,69,70,73,77,78,80,81,84,85,86,89', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '34,6,7,39,71,74,75,20,55,24,25', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,65,72,76,79,82,19,22,90,26,27,93,30,40,44,45,48,56', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '4,5,68,9,13,14,18,83,23,87,88,91,92,94,95,36,38,41,43,49,54']
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Text: 'C', X: 196.1701562102474, Y: 362.3356516441853, Width: 10.5, Height: 8
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Text: 'G', X: 213.6701562102474, Y: 362.3356516441853, Width: 10.5, Height: 8
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Text: 'C', X: 598.6701562102473, Y: 362.33565164418536, Width: 10.5, Height: 8
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Text: '50', X: 395.1163258065293, Y: 153.17125993211175, Width: 18.0, Height: 8
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Text: '70', X: 212.4201562102474, Y: 322.3356516441853, Width: 18.0, Height: 8
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Text: 'CLOCK, -9.7 ± 0.6
 kcal/mol, AUC: 0.595', X: 235.71007810512367, Y: 395.1356516441854, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 612.9201562102473, 395.1356516441854)
Updated viewBox: -0.25 0.0 618.1701562102473 400.1356516441854
Updated SVG: /disk1/www/rails/humanrnamap/public/result/268d3893-0510-4fc4-8ac8-bf21a6dec77d/final_image/CLOCK_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/268d3893-0510-4fc4-8ac8-bf21a6dec77d/final_image/CLOCK_fold_final_1.svg
