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/7b5e2aae-7e50-45b0-a91c-832591f197f6/final_image/TNRC18_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.72 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.72 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.72 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 173.37 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: 173.37 MB
Length of region: 81 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: 0.22 seconds
write dat - Current memory usage: 176.75 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/7b5e2aae-7e50-45b0-a91c-832591f197f6/fasta/TNRC18.fasta" "/disk1/www/rails/humanrnamap/public/result/7b5e2aae-7e50-45b0-a91c-832591f197f6/ct/TNRC18.ct" --SHAPE "TNRC18.dat"

fold - Elapsed time since the previous call: 0.09 seconds
fold - Current memory usage: 176.75 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/7b5e2aae-7e50-45b0-a91c-832591f197f6/ct/TNRC18.ct" "/disk1/www/rails/humanrnamap/public/result/7b5e2aae-7e50-45b0-a91c-832591f197f6/fold_FE/TNRC18.txt" -sh "TNRC18.dat"

efn2 - Elapsed time since the previous call: 0.46 seconds
efn2 - Current memory usage: 176.75 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/7b5e2aae-7e50-45b0-a91c-832591f197f6/ct/TNRC18.ct" 1 "/disk1/www/rails/humanrnamap/public/result/7b5e2aae-7e50-45b0-a91c-832591f197f6/fold_dbn/TNRC18_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 176.75 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CGUAACUGCAGCGCUGCCAGCUCCAGGGCGGCCUCACCGGCCUCCUCCUCCUCCUCCUCAUCCUCCUCCUCCUCCUCCUCC', '-structureDBN', '.....(((.(((.......))).)))((.((((.....)))).))....................................', '-o', '/disk1/www/rails/humanrnamap/public/result/7b5e2aae-7e50-45b0-a91c-832591f197f6/final_image/TNRC18_fold_1.svg', '-title', 'TNRC18, -18.9 ± 0.8\n kcal/mol, AUC: 0.675', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '64,2,3,67,70,7,8,73,11,76,13,15,16,79,20,22,26,27,28,30,31,34,39,40,43,46,49,52,55,58,61', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '32,33,66,41,42,44,18,50,51,29,62', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,68,69,6,71,74,75,77,80,17,21,45,47,48,53,56,57,63', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '65,4,5,72,9,10,12,14,78,81,19,23,24,25,35,36,37,38,54,59,60']
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Text: '1', X: 5.5, Y: 196.53152360604702, Width: 9.0, Height: 8
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Text: '10', X: 68.5, Y: 104.18045074588147, Width: 18.0, Height: 8
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Text: '30', X: 118.5, Y: 124.1804507458815, Width: 18.0, Height: 8
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Text: '40', X: 191.0, Y: 84.18045074588147, Width: 18.0, Height: 8
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Text: '50', X: 258.5, Y: 196.53152360604702, Width: 18.0, Height: 8
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Text: '60', X: 433.5, Y: 196.53152360604702, Width: 18.0, Height: 8
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Text: '81', X: 801.0, Y: 196.53152360604705, Width: 18.0, Height: 8
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Text: 'TNRC18, -18.9 ± 0.8
 kcal/mol, AUC: 0.675', X: 338.75, Y: 209.33152360604706, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 819.0, 209.33152360604706)
Updated viewBox: -0.25 0.0 824.25 214.33152360604706
Updated SVG: /disk1/www/rails/humanrnamap/public/result/7b5e2aae-7e50-45b0-a91c-832591f197f6/final_image/TNRC18_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/7b5e2aae-7e50-45b0-a91c-832591f197f6/final_image/TNRC18_fold_final_1.svg
