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/272aa9b5-a03c-44d2-867b-3eec1118c565/final_image/CLOCK_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.97 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.97 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.97 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.57 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: 172.57 MB
Length of region: 89 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: 176.31 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/272aa9b5-a03c-44d2-867b-3eec1118c565/fasta/CLOCK.fasta" "/disk1/www/rails/humanrnamap/public/result/272aa9b5-a03c-44d2-867b-3eec1118c565/ct/CLOCK.ct" --SHAPE "CLOCK.dat"

fold - Elapsed time since the previous call: 0.10 seconds
fold - Current memory usage: 176.31 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/272aa9b5-a03c-44d2-867b-3eec1118c565/ct/CLOCK.ct" "/disk1/www/rails/humanrnamap/public/result/272aa9b5-a03c-44d2-867b-3eec1118c565/fold_FE/CLOCK.txt" -sh "CLOCK.dat"

efn2 - Elapsed time since the previous call: 0.42 seconds
efn2 - Current memory usage: 176.31 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/272aa9b5-a03c-44d2-867b-3eec1118c565/ct/CLOCK.ct" 1 "/disk1/www/rails/humanrnamap/public/result/272aa9b5-a03c-44d2-867b-3eec1118c565/fold_dbn/CLOCK_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.31 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AAUGACCAUCCAGUAGAGAUUUCCCACAUUCCCAUGAAUAUCAAGAAUAGUUGUCAGAAUAUGUAUGUACCUGAGCAUAUGUACACAGA', '-structureDBN', '.....................((..(((.......................)))..)).(((((((((......)))))))))......', '-o', '/disk1/www/rails/humanrnamap/public/result/272aa9b5-a03c-44d2-867b-3eec1118c565/final_image/CLOCK_fold_1.svg', '-title', 'CLOCK, -9.9 ± 1.0\n kcal/mol, AUC: 0.767', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,4,9,13,14,16,18,20,21,22,29,30,35,36,39,41,45,48,50,51,52,53,54,57,60,62,63,64,66,67,68,72,73,75,78,80,81,82,88', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '32,33,7,8,79,83,55,23,24,25,26,27,28,61,31', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,65,69,38,6,70,10,76,77,15,89', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '2,5,71,74,11,12,17,19,84,85,86,87,34,37,40,42,43,44,46,47,49,56,58,59']
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Text: 'CLOCK, -9.9 ± 1.0
 kcal/mol, AUC: 0.767', X: 225.0, Y: 309.08072561282336, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 591.5, 309.08072561282336)
Updated viewBox: -0.25 -5.0 596.75 319.08072561282336
Updated SVG: /disk1/www/rails/humanrnamap/public/result/272aa9b5-a03c-44d2-867b-3eec1118c565/final_image/CLOCK_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/272aa9b5-a03c-44d2-867b-3eec1118c565/final_image/CLOCK_fold_final_1.svg
