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/77187ee9-7c69-4706-abad-ed25b5e6c2d2/final_image/HCFC1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.19 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.19 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.19 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.86 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: 172.86 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: 0.21 seconds
write dat - Current memory usage: 176.26 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/77187ee9-7c69-4706-abad-ed25b5e6c2d2/fasta/HCFC1.fasta" "/disk1/www/rails/humanrnamap/public/result/77187ee9-7c69-4706-abad-ed25b5e6c2d2/ct/HCFC1.ct" --SHAPE "HCFC1.dat"

fold - Elapsed time since the previous call: 0.10 seconds
fold - Current memory usage: 176.26 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/77187ee9-7c69-4706-abad-ed25b5e6c2d2/ct/HCFC1.ct" "/disk1/www/rails/humanrnamap/public/result/77187ee9-7c69-4706-abad-ed25b5e6c2d2/fold_FE/HCFC1.txt" -sh "HCFC1.dat"

efn2 - Elapsed time since the previous call: 0.46 seconds
efn2 - Current memory usage: 176.26 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/77187ee9-7c69-4706-abad-ed25b5e6c2d2/ct/HCFC1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/77187ee9-7c69-4706-abad-ed25b5e6c2d2/fold_dbn/HCFC1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.26 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AAAAGAAAAAAGGGGCAAGGAGCCCCGCGGCGGCCUGGGCAGCGCCUGUGCAGACCUCCCUGCAGGCCGCACUGCCAACUGCUGCA', '-structureDBN', '...........(((((.....)))))(((((((....((((((((((..((((......)))))))).))..))))..))))))).', '-o', '/disk1/www/rails/humanrnamap/public/result/77187ee9-7c69-4706-abad-ed25b5e6c2d2/final_image/HCFC1_fold_1.svg', '-title', 'HCFC1, -49.7 ± 1.3\n kcal/mol, AUC: 0.849', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '5,12,13,14,15,19,20,22,27,29,30,32,33,36,37,38,39,42,44,47,48,49,50,53,57,61,62,65,66,69,73,74,80,81,83,84', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '64,6,7,8,75,76,16,82,23,24,25,26,31,40,41,45,46,56,60,63', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,2,3,4,67,70,9,11,79,85,28,34,35,43,51,52,59', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '68,71,72,10,77,78,17,18,21,54,55,86,58']
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Text: 'HCFC1, -49.7 ± 1.3
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Calculated bounding box: (4.75, 4.999999999999943, 362.1351798356673, 515.52730386391)
Updated viewBox: -0.25 -5.684341886080802e-14 367.3851798356673 520.52730386391
Updated SVG: /disk1/www/rails/humanrnamap/public/result/77187ee9-7c69-4706-abad-ed25b5e6c2d2/final_image/HCFC1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/77187ee9-7c69-4706-abad-ed25b5e6c2d2/final_image/HCFC1_fold_final_1.svg
