Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 95% [================================================  ] \                     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/ac227eed-91fd-49fa-b8bf-f9616bb26ff9/final_image/CLOCK_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.77 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.77 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.77 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.31 MB
Based on canonical annotations, the following gene is in your area of interest: CLOCK(-)
write fasta - Elapsed time since the previous call: 0.66 seconds
write fasta - Current memory usage: 172.31 MB
Length of region: 94 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: 176.07 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/ac227eed-91fd-49fa-b8bf-f9616bb26ff9/fasta/CLOCK.fasta" "/disk1/www/rails/humanrnamap/public/result/ac227eed-91fd-49fa-b8bf-f9616bb26ff9/ct/CLOCK.ct" --SHAPE "CLOCK.dat"

fold - Elapsed time since the previous call: 0.12 seconds
fold - Current memory usage: 176.07 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/ac227eed-91fd-49fa-b8bf-f9616bb26ff9/ct/CLOCK.ct" "/disk1/www/rails/humanrnamap/public/result/ac227eed-91fd-49fa-b8bf-f9616bb26ff9/fold_FE/CLOCK.txt" -sh "CLOCK.dat"

efn2 - Elapsed time since the previous call: 0.49 seconds
efn2 - Current memory usage: 176.07 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/ac227eed-91fd-49fa-b8bf-f9616bb26ff9/ct/CLOCK.ct" 1 "/disk1/www/rails/humanrnamap/public/result/ac227eed-91fd-49fa-b8bf-f9616bb26ff9/fold_dbn/CLOCK_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 176.07 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CAGUCUGUUGGUUCAUCAUUAACACAGCCAGUGAUGUCUCAAGCUACAAAUUUACCAAUUCCACAAGGCAUGUCCCAGUUUCAGUUUUCAGCUC', '-structureDBN', '..((((..(((..(((((((.........)))))))........................)))..)))).........................', '-o', '/disk1/www/rails/humanrnamap/public/result/ac227eed-91fd-49fa-b8bf-f9616bb26ff9/final_image/CLOCK_fold_1.svg', '-title', 'CLOCK, -9.2 ± 0.9\n kcal/mol, AUC: 0.636', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,4,6,7,8,9,10,11,12,13,16,19,20,27,31,32,33,35,36,37,39,43,45,51,52,53,59,60,67,68,71,72,73,78,79,80,81,84,85,86,87,88,91,93', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '48,17,2,70,74,75,92', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '5,69,14,18,82,83,22,28,29,30,94,34,38,40,49,56,57,61,62,63', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,1,65,66,76,77,15,21,23,24,25,26,89,90,41,42,44,46,47,50,54,55,58']
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Text: 'C', X: 248.570846057526, Y: 334.20146150063624, Width: 10.5, Height: 8
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Text: 'U', X: 668.5708460575261, Y: 334.2014615006363, Width: 10.5, Height: 8
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Text: 'C', X: 686.0708460575261, Y: 334.2014615006363, Width: 10.5, Height: 8
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Text: '1', X: 181.820846057526, Y: 354.20146150063624, Width: 9.0, Height: 8
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Text: '50', X: 304.7882775582152, Y: 24.263529909471288, Width: 18.0, Height: 8
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Text: '60', X: 269.0892318615957, Y: 202.17874472213367, Width: 18.0, Height: 8
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Text: '80', X: 437.320846057526, Y: 354.2014615006363, Width: 18.0, Height: 8
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Text: '94', X: 682.3208460575261, Y: 354.2014615006363, Width: 18.0, Height: 8
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Text: 'CLOCK, -9.2 ± 0.9
 kcal/mol, AUC: 0.636', X: 279.41042302876303, Y: 367.0014615006363, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 700.3208460575261, 367.0014615006363)
Updated viewBox: -0.25 0.0 705.5708460575261 372.0014615006363
Updated SVG: /disk1/www/rails/humanrnamap/public/result/ac227eed-91fd-49fa-b8bf-f9616bb26ff9/final_image/CLOCK_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/ac227eed-91fd-49fa-b8bf-f9616bb26ff9/final_image/CLOCK_fold_final_1.svg
