Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 96% [================================================= ] -                     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/1b1d691d-5b72-4bb3-9b95-19abf06bb72f/final_image/HCFC1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.96 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.96 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.96 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.58 MB
Based on canonical annotations, the following gene is in your area of interest: HCFC1(-)
write fasta - Elapsed time since the previous call: 0.26 seconds
write fasta - Current memory usage: 172.58 MB
Length of region: 88 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: 175.99 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/1b1d691d-5b72-4bb3-9b95-19abf06bb72f/fasta/HCFC1.fasta" "/disk1/www/rails/humanrnamap/public/result/1b1d691d-5b72-4bb3-9b95-19abf06bb72f/ct/HCFC1.ct" --SHAPE "HCFC1.dat"

fold - Elapsed time since the previous call: 0.10 seconds
fold - Current memory usage: 175.99 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/1b1d691d-5b72-4bb3-9b95-19abf06bb72f/ct/HCFC1.ct" "/disk1/www/rails/humanrnamap/public/result/1b1d691d-5b72-4bb3-9b95-19abf06bb72f/fold_FE/HCFC1.txt" -sh "HCFC1.dat"

efn2 - Elapsed time since the previous call: 0.43 seconds
efn2 - Current memory usage: 175.99 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/1b1d691d-5b72-4bb3-9b95-19abf06bb72f/ct/HCFC1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/1b1d691d-5b72-4bb3-9b95-19abf06bb72f/fold_dbn/HCFC1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.03 seconds
ct2dot - Current memory usage: 175.99 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CGACAGUCUCAACGACCCAGCCAUUGAGAGCAAUUGCCUCAAUGAGCUGGCCGGCACGGUCCCCAGCACUGUGGCGCUGCUGCCCUCA', '-structureDBN', '.....(((.....)))((((((((((((.((....))))))))).)))))..((((((((.((((....)).)).)))).))))....', '-o', '/disk1/www/rails/humanrnamap/public/result/1b1d691d-5b72-4bb3-9b95-19abf06bb72f/final_image/HCFC1_fold_1.svg', '-title', 'HCFC1, -44.7 ± 0.9\n kcal/mol, AUC: 0.834', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,6,7,9,14,20,24,25,26,28,30,34,35,36,39,43,44,46,48,49,50,53,54,58,59,60,66,70,71,72,73,74,76,78,79,81,82,86', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '64,1,77,18,19,83,21,22,23,84,31,37,38,40,41,42,47,52,55,61', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '65,8,15,16,80,85,87,56,27,62,63', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '3,4,5,67,68,69,10,11,12,13,75,17,88,29,32,33,45,51,57']
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Text: 'A', X: 227.25, Y: 240.2878108726832, Width: 10.5, Height: 8
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Text: '88', X: 326.0, Y: 320.2878108726832, Width: 18.0, Height: 8
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Text: 'HCFC1, -44.7 ± 0.9
 kcal/mol, AUC: 0.834', X: 101.25, Y: 333.08781087268324, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 344.0, 333.08781087268324)
Updated viewBox: -0.25 0.0 349.25 338.08781087268324
Updated SVG: /disk1/www/rails/humanrnamap/public/result/1b1d691d-5b72-4bb3-9b95-19abf06bb72f/final_image/HCFC1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/1b1d691d-5b72-4bb3-9b95-19abf06bb72f/final_image/HCFC1_fold_final_1.svg
