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/6c6b7baf-729d-41f0-bcad-ee536aef6ad4/final_image/TNRC18_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.39 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.39 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.39 MB
read annotations - Elapsed time since the previous call: 0.10 seconds
read annotations - Current memory usage: 172.01 MB
Based on canonical annotations, the following gene is in your area of interest: TNRC18(-)
write fasta - Elapsed time since the previous call: 0.42 seconds
write fasta - Current memory usage: 172.01 MB
Length of region: 93 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: 175.04 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/6c6b7baf-729d-41f0-bcad-ee536aef6ad4/fasta/TNRC18.fasta" "/disk1/www/rails/humanrnamap/public/result/6c6b7baf-729d-41f0-bcad-ee536aef6ad4/ct/TNRC18.ct" --SHAPE "TNRC18.dat"

fold - Elapsed time since the previous call: 0.10 seconds
fold - Current memory usage: 175.04 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/6c6b7baf-729d-41f0-bcad-ee536aef6ad4/ct/TNRC18.ct" "/disk1/www/rails/humanrnamap/public/result/6c6b7baf-729d-41f0-bcad-ee536aef6ad4/fold_FE/TNRC18.txt" -sh "TNRC18.dat"

efn2 - Elapsed time since the previous call: 0.51 seconds
efn2 - Current memory usage: 175.04 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/6c6b7baf-729d-41f0-bcad-ee536aef6ad4/ct/TNRC18.ct" 1 "/disk1/www/rails/humanrnamap/public/result/6c6b7baf-729d-41f0-bcad-ee536aef6ad4/fold_dbn/TNRC18_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.04 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'ACCCGCAAGGAGGAGGCUCCCGAGAAUGUGGUCGAGAAGAAAGACUUGGAGUUGGAGAAGGAAGCCCCCAGCCCCUUCCAGGCCCUGUUCUCA', '-structureDBN', '........((((....)))).(((((((.((((..((((........((.(((((....((....)))))))))))))..)))).))))))).', '-o', '/disk1/www/rails/humanrnamap/public/result/6c6b7baf-729d-41f0-bcad-ee536aef6ad4/final_image/TNRC18_fold_1.svg', '-title', 'TNRC18, -32.2 ± 2.2\n kcal/mol, AUC: 0.691', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '5,9,10,12,13,15,16,18,22,24,27,28,29,30,31,32,34,36,39,43,46,47,48,49,51,52,53,54,55,57,60,61,64,71,76,77,81,82,86,87,88,89,91', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '1,2,3,65,66,67,68,72,75,78,17,84,85,90,92,50', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '4,70,73,74,14,79,83,20,21,23,26,33,37,44,45,56', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '69,6,7,8,11,80,19,25,93,35,38,40,41,42,58,59,62,63']
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Text: 'TNRC18, -32.2 ± 2.2
 kcal/mol, AUC: 0.691', X: 138.0977275632956, Y: 437.7878140728151, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 413.9454551265912, 437.7878140728151)
Updated viewBox: -0.25 0.0 419.1954551265912 442.7878140728151
Updated SVG: /disk1/www/rails/humanrnamap/public/result/6c6b7baf-729d-41f0-bcad-ee536aef6ad4/final_image/TNRC18_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/6c6b7baf-729d-41f0-bcad-ee536aef6ad4/final_image/TNRC18_fold_final_1.svg
