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/f964165f-d864-43e9-9876-ca71baf28c94/final_image/TFRC_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.35 MB
setup complete - Elapsed time since the previous call: 0.01 seconds
setup complete - Current memory usage: 159.35 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.35 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 173.00 MB
Based on canonical annotations, the following gene is in your area of interest: TFRC(-)
write fasta - Elapsed time since the previous call: 0.64 seconds
write fasta - Current memory usage: 173.00 MB
Length of region: 95 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: 176.71 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/f964165f-d864-43e9-9876-ca71baf28c94/fasta/TFRC.fasta" "/disk1/www/rails/humanrnamap/public/result/f964165f-d864-43e9-9876-ca71baf28c94/ct/TFRC.ct" --SHAPE "TFRC.dat"

fold - Elapsed time since the previous call: 0.11 seconds
fold - Current memory usage: 176.71 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/f964165f-d864-43e9-9876-ca71baf28c94/ct/TFRC.ct" "/disk1/www/rails/humanrnamap/public/result/f964165f-d864-43e9-9876-ca71baf28c94/fold_FE/TFRC.txt" -sh "TFRC.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 176.71 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/f964165f-d864-43e9-9876-ca71baf28c94/ct/TFRC.ct" 1 "/disk1/www/rails/humanrnamap/public/result/f964165f-d864-43e9-9876-ca71baf28c94/fold_dbn/TFRC_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.71 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'ACUCUACAUGUAGGAUGGUAACCUCAGAAAGCAAGAAUGUGAAGCUCACUGUGAGCAAUGUGCUGAAAGAGAUAAAAAUUCUUAACAUCUUUGGA', '-structureDBN', '..((((.(((((((((......(((....((((....(((...((.....))..)))...))))....)))......)))))..))))...))))', '-o', '/disk1/www/rails/humanrnamap/public/result/f964165f-d864-43e9-9876-ca71baf28c94/final_image/TFRC_fold_1.svg', '-title', 'TFRC, -9.6 ± 1.1\n kcal/mol, AUC: 0.537', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,5,9,10,11,13,14,16,17,18,19,24,27,31,35,38,39,40,41,44,46,50,51,52,53,55,59,60,61,62,64,65,69,71,73,79,80,82,83,88,90,91,92,93,94', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '74,76', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '77,47,15,84,85,54,87,56,89,95', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,2,4,6,7,8,12,20,21,22,23,25,26,28,29,30,32,33,34,36,37,42,43,45,48,49,57,58,63,66,67,68,70,72,75,78,81,86']
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Text: 'G', X: 325.2785046991191, Y: 129.08126478917694, Width: 10.5, Height: 8
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Text: 'A', X: 625.2911240508868, Y: 342.72530439600746, Width: 10.5, Height: 8
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Text: '40', X: 81.68959221077174, Y: 127.04161051663772, Width: 18.0, Height: 8
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Text: '50', X: 54.15856641965044, Y: 8.0, Width: 18.0, Height: 8
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Text: '60', X: 197.21328526570886, Y: 79.99396886214419, Width: 18.0, Height: 8
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Text: '90', X: 650.9213936985656, Y: 244.89264780669532, Width: 18.0, Height: 8
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Text: '95', X: 621.5411240508868, Y: 362.72530439600746, Width: 18.0, Height: 8
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Text: 'TFRC, -9.6 ± 1.1
 kcal/mol, AUC: 0.537', X: 254.21040484202, Y: 375.52530439600747, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 668.9213936985656, 375.52530439600747)
Updated viewBox: -0.25 -5.0 674.1713936985656 385.52530439600747
Updated SVG: /disk1/www/rails/humanrnamap/public/result/f964165f-d864-43e9-9876-ca71baf28c94/final_image/TFRC_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/f964165f-d864-43e9-9876-ca71baf28c94/final_image/TFRC_fold_final_1.svg
