Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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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/81dc0129-ec0b-4f01-a9d8-ead5a779f0f3/final_image/CLOCK_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.32 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.32 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.32 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.93 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: 172.93 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: 176.32 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/81dc0129-ec0b-4f01-a9d8-ead5a779f0f3/fasta/CLOCK.fasta" "/disk1/www/rails/humanrnamap/public/result/81dc0129-ec0b-4f01-a9d8-ead5a779f0f3/ct/CLOCK.ct" --SHAPE "CLOCK.dat"

fold - Elapsed time since the previous call: 0.12 seconds
fold - Current memory usage: 176.32 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/81dc0129-ec0b-4f01-a9d8-ead5a779f0f3/ct/CLOCK.ct" "/disk1/www/rails/humanrnamap/public/result/81dc0129-ec0b-4f01-a9d8-ead5a779f0f3/fold_FE/CLOCK.txt" -sh "CLOCK.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 176.32 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/81dc0129-ec0b-4f01-a9d8-ead5a779f0f3/ct/CLOCK.ct" 1 "/disk1/www/rails/humanrnamap/public/result/81dc0129-ec0b-4f01-a9d8-ead5a779f0f3/fold_dbn/CLOCK_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.32 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CAUGGUACCUAGUACUAUGCUUAUGGGCCAGGUGGUGACUGCAUAUCCUACUUUUGCUACACAACAGCAACAGUCACAGACAUUGUCAGUAACGC', '-structureDBN', '((((((((...)))))))).((((.(((...((.(((((((............(((((.......))))))))))))..))...))).))))...', '-o', '/disk1/www/rails/humanrnamap/public/result/81dc0129-ec0b-4f01-a9d8-ead5a779f0f3/final_image/CLOCK_fold_1.svg', '-title', 'CLOCK, -26.6 ± 1.4\n kcal/mol, AUC: 0.79', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,4,5,6,10,12,13,16,18,19,21,22,24,25,26,27,31,32,33,34,35,36,37,40,41,44,46,49,52,53,54,55,56,58,67,73,74,79,83,84,85,86,89,90,94', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '1,2,66,68,38,39,72,57,28,29', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '69,7,8,9,76,45,15,48,17,80,23,88,30', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,65,70,71,11,75,77,14,78,81,82,20,87,91,92,93,95,42,43,47,50,51,59,60,61,62,63']
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Text: 'CLOCK, -26.6 ± 1.4
 kcal/mol, AUC: 0.79', X: 55.05350167496508, Y: 515.8800288112445, Width: 133.5, Height: 23
Calculated bounding box: (4.75, 5.684341886080802e-14, 238.85700334993015, 515.8800288112445)
Updated viewBox: -0.25 -4.999999999999943 244.10700334993015 525.8800288112445
Updated SVG: /disk1/www/rails/humanrnamap/public/result/81dc0129-ec0b-4f01-a9d8-ead5a779f0f3/final_image/CLOCK_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/81dc0129-ec0b-4f01-a9d8-ead5a779f0f3/final_image/CLOCK_fold_final_1.svg
