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/3c02a489-7c71-4df3-8647-07aaa14523e2/final_image/C9orf72_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.84 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.84 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.84 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.47 MB
Based on canonical annotations, the following gene is in your area of interest: C9orf72(-)
write fasta - Elapsed time since the previous call: 0.38 seconds
write fasta - Current memory usage: 172.47 MB
Length of region: 106 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: 175.87 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/3c02a489-7c71-4df3-8647-07aaa14523e2/fasta/C9orf72.fasta" "/disk1/www/rails/humanrnamap/public/result/3c02a489-7c71-4df3-8647-07aaa14523e2/ct/C9orf72.ct" --SHAPE "C9orf72.dat"

fold - Elapsed time since the previous call: 0.15 seconds
fold - Current memory usage: 175.87 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/3c02a489-7c71-4df3-8647-07aaa14523e2/ct/C9orf72.ct" "/disk1/www/rails/humanrnamap/public/result/3c02a489-7c71-4df3-8647-07aaa14523e2/fold_FE/C9orf72.txt" -sh "C9orf72.dat"

efn2 - Elapsed time since the previous call: 0.51 seconds
efn2 - Current memory usage: 175.87 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/3c02a489-7c71-4df3-8647-07aaa14523e2/ct/C9orf72.ct" 1 "/disk1/www/rails/humanrnamap/public/result/3c02a489-7c71-4df3-8647-07aaa14523e2/fold_dbn/C9orf72_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.03 seconds
ct2dot - Current memory usage: 175.87 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CAGAUAGUUGACUUUCUAUCUUUUGGCAUUCUUUGGUGUGUAGAAUUACUGUAAUACUUCUGCAAUCAACUGAAAACUAGAGCCUUUAAAUGAUUUCAAUUCCACA', '-structureDBN', '.((((((........)))))).((((..(((.(((((.(((((((.((......)).))))))))))))..)))..))))..........................', '-o', '/disk1/www/rails/humanrnamap/public/result/3c02a489-7c71-4df3-8647-07aaa14523e2/final_image/C9orf72_fold_1.svg', '-title', 'C9orf72, -19.5 ± 1.2\n kcal/mol, AUC: 0.657', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,5,7,8,9,10,13,14,15,17,19,21,22,23,24,25,26,29,30,32,33,34,35,36,37,38,39,40,41,43,46,47,50,51,52,55,58,59,61,62,66,71,72,78,80,82,85,86,87,91,92,94,95,96,100,101', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '97,2,99,6,102,103,79,20,88,60,63', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '64,1,65,69,73,74,75,18,83,98,104,42,106,45,48,53', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '67,4,68,70,11,12,76,77,16,81,84,89,90,27,28,93,31,105,44,49,54,56,57']
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Text: '70', X: 141.5296391263204, Y: 324.05194099978974, Width: 18.0, Height: 8
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Text: 'C9orf72, -19.5 ± 1.2
 kcal/mol, AUC: 0.657', X: 225.0, Y: 544.94384951917, Width: 142.5, Height: 24
Calculated bounding box: (-3.874396344562559, 5.0, 596.0, 544.94384951917)
Updated viewBox: -8.874396344562559 0.0 609.8743963445626 549.94384951917
Updated SVG: /disk1/www/rails/humanrnamap/public/result/3c02a489-7c71-4df3-8647-07aaa14523e2/final_image/C9orf72_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/3c02a489-7c71-4df3-8647-07aaa14523e2/final_image/C9orf72_fold_final_1.svg
