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/0dff1523-e14e-4be0-9e15-9f2b705a5862/final_image/TNRC18_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.88 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.88 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.88 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.44 MB
Based on canonical annotations, the following gene is in your area of interest: TNRC18(-)
write fasta - Elapsed time since the previous call: 0.57 seconds
write fasta - Current memory usage: 172.44 MB
Length of region: 96 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: 176.14 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/0dff1523-e14e-4be0-9e15-9f2b705a5862/fasta/TNRC18.fasta" "/disk1/www/rails/humanrnamap/public/result/0dff1523-e14e-4be0-9e15-9f2b705a5862/ct/TNRC18.ct" --SHAPE "TNRC18.dat"

fold - Elapsed time since the previous call: 0.12 seconds
fold - Current memory usage: 176.14 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/0dff1523-e14e-4be0-9e15-9f2b705a5862/ct/TNRC18.ct" "/disk1/www/rails/humanrnamap/public/result/0dff1523-e14e-4be0-9e15-9f2b705a5862/fold_FE/TNRC18.txt" -sh "TNRC18.dat"

efn2 - Elapsed time since the previous call: 0.42 seconds
efn2 - Current memory usage: 176.14 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/0dff1523-e14e-4be0-9e15-9f2b705a5862/ct/TNRC18.ct" 1 "/disk1/www/rails/humanrnamap/public/result/0dff1523-e14e-4be0-9e15-9f2b705a5862/fold_dbn/TNRC18_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.14 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CAAGGCCCGCAAGCUCUUCUACAAGGCCAUCGUGCGCGGCAAGGAGAUGAUCCGUAUCGGGGACUGUGCCGUGUUCCUCUCUGCCGGCCGCCCCAA', '-structureDBN', '....(((((((.((.(((....))))).....)))).)))..(((.....))).....((((..((.((((.((........))))))))))))..', '-o', '/disk1/www/rails/humanrnamap/public/result/0dff1523-e14e-4be0-9e15-9f2b705a5862/final_image/TNRC18_fold_1.svg', '-title', 'TNRC18, -34.8 ± 1.1\n kcal/mol, AUC: 0.848', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '4,5,9,13,15,17,18,20,25,26,30,32,33,34,36,38,39,43,44,46,48,49,51,54,55,57,59,60,61,62,65,66,67,68,71,72,73,74,75,78,80,82,83,86,87,90', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '1,69,6,88,91,14,93,85,24,89,27,92,29', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '64,70,7,8,11,77,16,19,84,28,94,37,40,52,53,63', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '2,3,10,12,76,79,81,21,22,23,31,95,96,35,41,42,45,47,50,56,58']
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Text: 'TNRC18, -34.8 ± 1.1
 kcal/mol, AUC: 0.848', X: 258.5922530683859, Y: 238.0386092942796, Width: 142.5, Height: 23
Calculated bounding box: (-4.0, 5.0, 647.1818025475586, 238.0386092942796)
Updated viewBox: -9.0 0.0 661.1818025475586 243.0386092942796
Updated SVG: /disk1/www/rails/humanrnamap/public/result/0dff1523-e14e-4be0-9e15-9f2b705a5862/final_image/TNRC18_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/0dff1523-e14e-4be0-9e15-9f2b705a5862/final_image/TNRC18_fold_final_1.svg
