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/948e160c-1bd3-41e6-ad7d-80d3861fac8e/final_image/CLOCK_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.17 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.17 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.17 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.79 MB
Based on canonical annotations, the following gene is in your area of interest: CLOCK(-)
write fasta - Elapsed time since the previous call: 0.64 seconds
write fasta - Current memory usage: 172.79 MB
Length of region: 113 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: 176.34 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/948e160c-1bd3-41e6-ad7d-80d3861fac8e/fasta/CLOCK.fasta" "/disk1/www/rails/humanrnamap/public/result/948e160c-1bd3-41e6-ad7d-80d3861fac8e/ct/CLOCK.ct" --SHAPE "CLOCK.dat"

fold - Elapsed time since the previous call: 0.16 seconds
fold - Current memory usage: 176.34 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/948e160c-1bd3-41e6-ad7d-80d3861fac8e/ct/CLOCK.ct" "/disk1/www/rails/humanrnamap/public/result/948e160c-1bd3-41e6-ad7d-80d3861fac8e/fold_FE/CLOCK.txt" -sh "CLOCK.dat"

efn2 - Elapsed time since the previous call: 0.45 seconds
efn2 - Current memory usage: 176.34 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/948e160c-1bd3-41e6-ad7d-80d3861fac8e/ct/CLOCK.ct" 1 "/disk1/www/rails/humanrnamap/public/result/948e160c-1bd3-41e6-ad7d-80d3861fac8e/fold_dbn/CLOCK_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.34 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'ACCUACAUUCCUUAGUAAUGAAGAGUUUACACAAUUAAUGUUAGAGGCUCUUGAUGGUUUUUUUUUAGCAAUCAUGACAGAUGGAAGCAUAAUAUAUGUGUCUGAGAGUGUAA', '-structureDBN', '...(((((((.((((..((.((((((((..(((.....)))...)))))))).)).((((((.(((..((....))..))).)))))).............))))))))))).', '-o', '/disk1/www/rails/humanrnamap/public/result/948e160c-1bd3-41e6-ad7d-80d3861fac8e/final_image/CLOCK_fold_1.svg', '-title', 'CLOCK, -15.3 ± 1.4\n kcal/mol, AUC: 0.572', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '4,8,9,12,13,15,16,19,20,23,25,26,27,28,35,36,39,40,41,42,44,46,47,49,51,52,53,55,56,57,58,59,60,61,62,63,64,65,66,68,72,75,76,80,82,83,84,87,90,93,95,97,98,99,100,101,103,104,106,108,109,110,111', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '18,85,21,31', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '3,67,7,73,10,11,77,14,79,17,22,86,24,88,89,29,30,37,43,48,112,50,113,54', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,2,5,6,69,70,71,74,78,81,91,92,94,32,33,34,96,38,102,105,107,45']
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Text: '70', X: 214.289969695015, Y: 49.204809539522444, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 319.77586120589893, Y: 104.26411779591206, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '90', X: 411.2399766906807, Y: 230.70541470161118, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '100', X: 409.3735303126177, Y: 400.5176522161497, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '110', X: 359.26329834653006, Y: 534.7313381287177, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '113', X: 356.76329834653006, Y: 594.7313381287177, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'CLOCK, -15.3 ± 1.4
 kcal/mol, AUC: 0.572', X: 166.02503778884142, Y: 607.5313381287176, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 469.80007557768283, 607.5313381287176)
Updated viewBox: -0.25 0.0 475.05007557768283 612.5313381287176
Updated SVG: /disk1/www/rails/humanrnamap/public/result/948e160c-1bd3-41e6-ad7d-80d3861fac8e/final_image/CLOCK_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/948e160c-1bd3-41e6-ad7d-80d3861fac8e/final_image/CLOCK_fold_final_1.svg
