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/1bff0723-9764-4300-8a13-108b3c1eae3a/final_image/TFRC_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.23 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.23 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.23 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.82 MB
Based on canonical annotations, the following gene is in your area of interest: TFRC(-)
write fasta - Elapsed time since the previous call: 1.13 seconds
write fasta - Current memory usage: 172.82 MB
Length of region: 107 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: 176.23 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/1bff0723-9764-4300-8a13-108b3c1eae3a/fasta/TFRC.fasta" "/disk1/www/rails/humanrnamap/public/result/1bff0723-9764-4300-8a13-108b3c1eae3a/ct/TFRC.ct" --SHAPE "TFRC.dat"

fold - Elapsed time since the previous call: 0.13 seconds
fold - Current memory usage: 176.23 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/1bff0723-9764-4300-8a13-108b3c1eae3a/ct/TFRC.ct" "/disk1/www/rails/humanrnamap/public/result/1bff0723-9764-4300-8a13-108b3c1eae3a/fold_FE/TFRC.txt" -sh "TFRC.dat"

efn2 - Elapsed time since the previous call: 0.40 seconds
efn2 - Current memory usage: 176.23 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/1bff0723-9764-4300-8a13-108b3c1eae3a/ct/TFRC.ct" 1 "/disk1/www/rails/humanrnamap/public/result/1bff0723-9764-4300-8a13-108b3c1eae3a/fold_dbn/TFRC_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.23 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'ACUCACUUUAGACAAUGCUGCUUUCCCUUUCCUUGCAUAUUCUGGAAUCCCAGCAGUUUCUUUCUGUUUUUGCGAGGACACAGAUUAUCCUUAUUUGGGUACCACCA', '-structureDBN', '.......................((....((((((((....((((....))))(((.......)))....))))))))....)).(((((......)))))......', '-o', '/disk1/www/rails/humanrnamap/public/result/1bff0723-9764-4300-8a13-108b3c1eae3a/final_image/TFRC_fold_1.svg', '-title', 'TFRC, -18.7 ± 1.0\n kcal/mol, AUC: 0.612', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,7,8,9,11,16,17,19,20,22,23,24,28,29,30,33,34,35,38,40,41,43,44,45,48,53,56,57,58,59,61,62,63,65,66,67,68,69,70,71,72,74,76,77,83,85,86,88,91,92,94,95,96,97,98,99,100', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '103,75,78,46,51,87,90,93', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,4,5,73,12,15,80,18,82,25,37,39,42,106,107,47,49,52,55', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,2,6,10,13,14,79,81,84,21,89,26,27,31,32,36,101,102,104,105,50,54,60']
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Text: 'TFRC, -18.7 ± 1.0
 kcal/mol, AUC: 0.612', X: 242.5, Y: 447.49151024859344, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 631.0, 447.49151024859344)
Updated viewBox: -0.25 -5.0 636.25 457.49151024859344
Updated SVG: /disk1/www/rails/humanrnamap/public/result/1bff0723-9764-4300-8a13-108b3c1eae3a/final_image/TFRC_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/1bff0723-9764-4300-8a13-108b3c1eae3a/final_image/TFRC_fold_final_1.svg
