Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 98% [==================================================] -                     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/d60959cb-3335-45e1-9d89-33ef5deb746f/final_image/CLOCK_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.36 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.36 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.36 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 173.01 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: 173.01 MB
Length of region: 86 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: 0.20 seconds
write dat - Current memory usage: 176.13 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/d60959cb-3335-45e1-9d89-33ef5deb746f/fasta/CLOCK.fasta" "/disk1/www/rails/humanrnamap/public/result/d60959cb-3335-45e1-9d89-33ef5deb746f/ct/CLOCK.ct" --SHAPE "CLOCK.dat"

fold - Elapsed time since the previous call: 0.10 seconds
fold - Current memory usage: 176.13 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/d60959cb-3335-45e1-9d89-33ef5deb746f/ct/CLOCK.ct" "/disk1/www/rails/humanrnamap/public/result/d60959cb-3335-45e1-9d89-33ef5deb746f/fold_FE/CLOCK.txt" -sh "CLOCK.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 176.13 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/d60959cb-3335-45e1-9d89-33ef5deb746f/ct/CLOCK.ct" 1 "/disk1/www/rails/humanrnamap/public/result/d60959cb-3335-45e1-9d89-33ef5deb746f/fold_dbn/CLOCK_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 176.13 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'ACUGUAUAACACUAUGGUGAUUUCUCAGCCUGCAGCCGGAAGCAUGGUCCAGAUUCCAUCUAGUAUGCCACAAAACAGCACCCAGA', '-structureDBN', '..........((((.((((...(((..((((((........))).)))..)))...)))))))).(((.........)))......', '-o', '/disk1/www/rails/humanrnamap/public/result/d60959cb-3335-45e1-9d89-33ef5deb746f/final_image/CLOCK_fold_1.svg', '-title', 'CLOCK, -15.8 ± 0.8\n kcal/mol, AUC: 0.694', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,4,5,7,13,15,16,17,18,19,21,22,23,25,28,31,32,35,38,39,42,45,46,47,48,52,54,55,59,61,63,64,66,67,78,85', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '36,76,77,14,79,80,81,82,57,30', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '33,34,68,37,69,73,43,44,49,58,60,29', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,2,65,6,70,8,9,10,11,12,71,72,74,75,83,20,84,86,24,26,27,40,41,50,51,53,56,62']
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Text: 'CLOCK, -15.8 ± 0.8
 kcal/mol, AUC: 0.694', X: 128.75, Y: 470.35951403113677, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 399.0, 470.35951403113677)
Updated viewBox: -0.25 0.0 404.25 475.35951403113677
Updated SVG: /disk1/www/rails/humanrnamap/public/result/d60959cb-3335-45e1-9d89-33ef5deb746f/final_image/CLOCK_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/d60959cb-3335-45e1-9d89-33ef5deb746f/final_image/CLOCK_fold_final_1.svg
