Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 96% [================================================= ] -                     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/85acc2c5-d406-4839-8c95-5e0cab842c4b/final_image/PLEKHM2_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.46 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.46 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.46 MB
read annotations - Elapsed time since the previous call: 0.10 seconds
read annotations - Current memory usage: 171.99 MB
Based on canonical annotations, the following gene is in your area of interest: PLEKHM2(+)
write fasta - Elapsed time since the previous call: 2.19 seconds
write fasta - Current memory usage: 171.99 MB
Length of region: 88 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: 175.32 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/85acc2c5-d406-4839-8c95-5e0cab842c4b/fasta/PLEKHM2.fasta" "/disk1/www/rails/humanrnamap/public/result/85acc2c5-d406-4839-8c95-5e0cab842c4b/ct/PLEKHM2.ct" --SHAPE "PLEKHM2.dat"

fold - Elapsed time since the previous call: 0.14 seconds
fold - Current memory usage: 175.32 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/85acc2c5-d406-4839-8c95-5e0cab842c4b/ct/PLEKHM2.ct" "/disk1/www/rails/humanrnamap/public/result/85acc2c5-d406-4839-8c95-5e0cab842c4b/fold_FE/PLEKHM2.txt" -sh "PLEKHM2.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 175.32 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/85acc2c5-d406-4839-8c95-5e0cab842c4b/ct/PLEKHM2.ct" 1 "/disk1/www/rails/humanrnamap/public/result/85acc2c5-d406-4839-8c95-5e0cab842c4b/fold_dbn/PLEKHM2_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 175.32 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AACCUCCCUACCCCAGCAUCCUGACGGAUGCCACCAUGGAGAAGCUGGCACUGGCCAAAUUUGUGGCCCAAGAAUCGAAGUGUGAGGC', '-structureDBN', '...((((........((((((....))))))......))))...((.((((((((((......)))))..........))))).))..', '-o', '/disk1/www/rails/humanrnamap/public/result/85acc2c5-d406-4839-8c95-5e0cab842c4b/final_image/PLEKHM2_fold_1.svg', '-title', 'PLEKHM2, -31.9 ± 1.2\n kcal/mol, AUC: 0.846', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '5,9,16,19,22,23,26,27,29,30,37,38,39,41,44,46,47,48,52,53,54,60,61,62,63,64,65,66,72,75,77,80,81,82,83,84,86,87', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '6,7,17,18,20,21,55,88,57,28,31', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '67,4,36,68,8,43,13,45,49,56', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,2,3,69,70,71,73,10,11,12,74,14,15,76,78,79,85,24,25,32,33,34,35,40,42,50,51,58,59']
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Text: '88', X: 223.5, Y: 322.85600539243103, Width: 18.0, Height: 8
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Text: 'PLEKHM2, -31.9 ± 1.2
 kcal/mol, AUC: 0.846', X: 47.0, Y: 335.65600539243104, Width: 148.5, Height: 23
Calculated bounding box: (-1.7275992374360918, 5.0, 241.5, 335.65600539243104)
Updated viewBox: -6.727599237436092 0.0 253.2275992374361 340.65600539243104
Updated SVG: /disk1/www/rails/humanrnamap/public/result/85acc2c5-d406-4839-8c95-5e0cab842c4b/final_image/PLEKHM2_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/85acc2c5-d406-4839-8c95-5e0cab842c4b/final_image/PLEKHM2_fold_final_1.svg
