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/c6f641f7-cb25-4a88-9208-6955f697143a/final_image/CLOCK_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.98 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.98 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.98 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.55 MB
Based on canonical annotations, the following gene is in your area of interest: CLOCK(-)
write fasta - Elapsed time since the previous call: 0.33 seconds
write fasta - Current memory usage: 172.55 MB
Length of region: 108 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: 176.21 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/c6f641f7-cb25-4a88-9208-6955f697143a/fasta/CLOCK.fasta" "/disk1/www/rails/humanrnamap/public/result/c6f641f7-cb25-4a88-9208-6955f697143a/ct/CLOCK.ct" --SHAPE "CLOCK.dat"

fold - Elapsed time since the previous call: 0.15 seconds
fold - Current memory usage: 176.21 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/c6f641f7-cb25-4a88-9208-6955f697143a/ct/CLOCK.ct" "/disk1/www/rails/humanrnamap/public/result/c6f641f7-cb25-4a88-9208-6955f697143a/fold_FE/CLOCK.txt" -sh "CLOCK.dat"

efn2 - Elapsed time since the previous call: 0.42 seconds
efn2 - Current memory usage: 176.21 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/c6f641f7-cb25-4a88-9208-6955f697143a/ct/CLOCK.ct" 1 "/disk1/www/rails/humanrnamap/public/result/c6f641f7-cb25-4a88-9208-6955f697143a/fold_dbn/CLOCK_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.21 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AUUCAGGGUUAUUUGAGGGGAAAAAACCCCAUAGUGCCUUGAUUUUAAUUCAGGUGAUAACUCACCAUCUUGAAGUCAUUGUCCGGUUUCCGUAGCAGUUUUGAAACC', '-structureDBN', '.....((((...(((.((((......)))).))).)))).((((((((....(((((....)))))...)))))))).......((((((............))))))', '-o', '/disk1/www/rails/humanrnamap/public/result/c6f641f7-cb25-4a88-9208-6955f697143a/final_image/CLOCK_fold_1.svg', '-title', 'CLOCK, -35.3 ± 1.0\n kcal/mol, AUC: 0.913', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,6,7,8,9,10,12,13,14,15,17,18,19,20,32,34,35,36,39,40,41,43,44,45,46,49,50,53,54,55,56,58,62,68,70,71,72,75,76,79,80,81,82,85,86,87,88,89,92,93,95,98,99,100,101,102,103', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '66,37,38,104,42,21,27,28,29,30,63', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '64,65,5,73,74,11,22,90,94,33,105,106,107,108,47,57', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,67,4,69,77,78,16,83,84,23,24,25,26,91,31,96,97,48,51,52,59,60,61']
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Text: 'CLOCK, -35.3 ± 1.0
 kcal/mol, AUC: 0.913', X: 131.42745015593988, Y: 364.9135766041669, Width: 142.5, Height: 23
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Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/c6f641f7-cb25-4a88-9208-6955f697143a/final_image/CLOCK_fold_final_1.svg
