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/d3172b8a-dcc3-4606-b313-25e2b0e6d4e8/final_image/CLOCK_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.06 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.06 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.06 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 171.74 MB
Based on canonical annotations, the following gene is in your area of interest: CLOCK(-)
write fasta - Elapsed time since the previous call: 0.34 seconds
write fasta - Current memory usage: 171.74 MB
Length of region: 125 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: 0.21 seconds
write dat - Current memory usage: 174.85 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/d3172b8a-dcc3-4606-b313-25e2b0e6d4e8/fasta/CLOCK.fasta" "/disk1/www/rails/humanrnamap/public/result/d3172b8a-dcc3-4606-b313-25e2b0e6d4e8/ct/CLOCK.ct" --SHAPE "CLOCK.dat"

fold - Elapsed time since the previous call: 0.20 seconds
fold - Current memory usage: 174.85 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/d3172b8a-dcc3-4606-b313-25e2b0e6d4e8/ct/CLOCK.ct" "/disk1/www/rails/humanrnamap/public/result/d3172b8a-dcc3-4606-b313-25e2b0e6d4e8/fold_FE/CLOCK.txt" -sh "CLOCK.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 174.85 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/d3172b8a-dcc3-4606-b313-25e2b0e6d4e8/ct/CLOCK.ct" 1 "/disk1/www/rails/humanrnamap/public/result/d3172b8a-dcc3-4606-b313-25e2b0e6d4e8/fold_dbn/CLOCK_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 174.85 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AACUUUUUAAAAGUGGAAUGCAAAUAGCAUUUUACUUUAGUAUUUCUGCUUUUUUCUUUCUGUUUCUUUGGUAAUUGAAAGUUUGUUGAUGAAUAUUUGUGUAAAACGCAUUCAAGUCUAUAACC', '-structureDBN', '..........(((((((((((.....))))))))))).((((....)))).....(((((.(((........))).))))).((((.(((.......(((((...))))).....))).))))..', '-o', '/disk1/www/rails/humanrnamap/public/result/d3172b8a-dcc3-4606-b313-25e2b0e6d4e8/final_image/CLOCK_fold_1.svg', '-title', 'CLOCK, -26.4 ± 1.2\n kcal/mol, AUC: 0.724', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '4,5,6,7,8,13,14,15,16,19,20,25,27,30,31,32,33,36,37,38,40,41,43,44,45,47,48,50,51,52,53,54,55,57,58,59,61,62,63,64,65,67,68,69,70,71,72,75,76,77,81,82,83,84,85,86,87,88,90,91,94,96,97,98,99,100,101,102,108,111,112,116,117,119,121', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '34,35,9,12,17,18,21,125,56,28,29', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,2,3,39,104,73,10,11,79,80,49,124,120,122,60', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '66,74,78,22,23,24,89,26,92,93,95,103,105,42,106,107,109,46,110,113,114,115,118,123']
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Text: '10', X: 158.5, Y: 355.84629369960714, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 156.0, Y: 155.84629369960717, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 228.5, Y: 195.84629369960717, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 223.5, Y: 315.84629369960714, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 290.14213562373095, Y: 349.98842932333815, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 361.0, Y: 255.8462936996072, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 435.8743963445626, Y: 124.16303409350357, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 433.5, Y: 315.8462936996072, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '90', X: 430.4231305735006, Y: 212.05248627515718, Width: 18.0, Height: 8
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Warning: Font Verdana not found. Using default font.
Text: '110', X: 511.6975082388541, Y: 116.25543572310704, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '120', X: 496.5, Y: 275.8462936996072, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '125', X: 511.5, Y: 355.8462936996072, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'CLOCK, -26.4 ± 1.2
 kcal/mol, AUC: 0.724', X: 202.82810811600046, Y: 368.6462936996072, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 543.4062162320009, 368.6462936996072)
Updated viewBox: -0.25 0.0 548.6562162320009 373.6462936996072
Updated SVG: /disk1/www/rails/humanrnamap/public/result/d3172b8a-dcc3-4606-b313-25e2b0e6d4e8/final_image/CLOCK_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/d3172b8a-dcc3-4606-b313-25e2b0e6d4e8/final_image/CLOCK_fold_final_1.svg
