Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 97% [================================================= ] \                     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/187e209f-663d-42b5-b5a5-6475ebd9c888/final_image/LMNA_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 156.59 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 156.59 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 156.59 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 170.16 MB
Based on canonical annotations, the following gene is in your area of interest: LMNA(+)
write fasta - Elapsed time since the previous call: 2.01 seconds
write fasta - Current memory usage: 170.16 MB
Length of region: 92 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: 0.17 seconds
write dat - Current memory usage: 173.52 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/187e209f-663d-42b5-b5a5-6475ebd9c888/fasta/LMNA.fasta" "/disk1/www/rails/humanrnamap/public/result/187e209f-663d-42b5-b5a5-6475ebd9c888/ct/LMNA.ct" --SHAPE "LMNA.dat"

fold - Elapsed time since the previous call: 0.11 seconds
fold - Current memory usage: 173.52 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/187e209f-663d-42b5-b5a5-6475ebd9c888/ct/LMNA.ct" "/disk1/www/rails/humanrnamap/public/result/187e209f-663d-42b5-b5a5-6475ebd9c888/fold_FE/LMNA.txt" -sh "LMNA.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 173.52 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/187e209f-663d-42b5-b5a5-6475ebd9c888/ct/LMNA.ct" 1 "/disk1/www/rails/humanrnamap/public/result/187e209f-663d-42b5-b5a5-6475ebd9c888/fold_dbn/LMNA_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 173.52 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CAAGCUCUUGGAGGGCGAGGAGGAGAGGCUACGCCUGUCCCCCAGCCCUACCUCGCAGCGCAGCCGUGGCCGUGCUUCCUCUCACUCAUCCC', '-structureDBN', '.........(((((((..((.(((.((((...)))).)))))..))))).))....(((((.((....)).)))))................', '-o', '/disk1/www/rails/humanrnamap/public/result/187e209f-663d-42b5-b5a5-6475ebd9c888/final_image/LMNA_fold_1.svg', '-title', 'LMNA, -41.6 ± 1.0\n kcal/mol, AUC: 0.82', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '4,6,8,9,10,11,13,14,15,17,19,20,22,23,25,27,28,30,33,36,37,38,45,49,53,55,58,60,63,66,67,68,69,72,73,74,76,77,80,82,86,89', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '70,79,16,21,24,26,34,35,39,40,42,43,46,47,48,52', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '64,1,7,75,78,81,83,84,85,87,88,90,91,29,41,50,51,54,57,59,61', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '32,65,2,3,5,71,12,44,18,56,92,62,31']
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Text: '60', X: 258.5, Y: 311.1205071807655, Width: 18.0, Height: 8
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Text: '70', X: 331.0, Y: 258.76943432059994, Width: 18.0, Height: 8
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Text: '92', X: 591.0, Y: 391.1205071807655, Width: 18.0, Height: 8
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Text: 'LMNA, -41.6 ± 1.0
 kcal/mol, AUC: 0.82', X: 238.25, Y: 403.9205071807655, Width: 133.5, Height: 23
Calculated bounding box: (4.75, 2.862960720867875, 609.0, 403.9205071807655)
Updated viewBox: -0.25 -2.137039279132125 614.25 411.05754645989765
Updated SVG: /disk1/www/rails/humanrnamap/public/result/187e209f-663d-42b5-b5a5-6475ebd9c888/final_image/LMNA_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/187e209f-663d-42b5-b5a5-6475ebd9c888/final_image/LMNA_fold_final_1.svg
