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/6c2b6901-a6c6-4213-9eca-6a9f41cfac5f/final_image/MALAT1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.65 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.65 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.65 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.25 MB
Based on canonical annotations, the following gene is in your area of interest: MALAT1(+)
write fasta - Elapsed time since the previous call: 0.53 seconds
write fasta - Current memory usage: 172.25 MB
Length of region: 113 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: 175.67 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/6c2b6901-a6c6-4213-9eca-6a9f41cfac5f/fasta/MALAT1.fasta" "/disk1/www/rails/humanrnamap/public/result/6c2b6901-a6c6-4213-9eca-6a9f41cfac5f/ct/MALAT1.ct" --SHAPE "MALAT1.dat"

fold - Elapsed time since the previous call: 0.16 seconds
fold - Current memory usage: 175.67 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/6c2b6901-a6c6-4213-9eca-6a9f41cfac5f/ct/MALAT1.ct" "/disk1/www/rails/humanrnamap/public/result/6c2b6901-a6c6-4213-9eca-6a9f41cfac5f/fold_FE/MALAT1.txt" -sh "MALAT1.dat"

efn2 - Elapsed time since the previous call: 0.42 seconds
efn2 - Current memory usage: 175.67 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/6c2b6901-a6c6-4213-9eca-6a9f41cfac5f/ct/MALAT1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/6c2b6901-a6c6-4213-9eca-6a9f41cfac5f/fold_dbn/MALAT1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.67 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CGUUGUGCGUAGAGGAUCCUAGACCAGCAUGCCAGUGUGCCAAGGCCACAGGGAAAGCGAGUGGUUGGUAAAAAUCCGUGAGGUCGGCAAUAUGUUGUUUUUCUGGAACUUAC', '-structureDBN', '(((((.((((...((........))...)))))))))(((((..(((((...........))))))))))....((((.((((.((((.....))))..))))))))......', '-o', '/disk1/www/rails/humanrnamap/public/result/6c2b6901-a6c6-4213-9eca-6a9f41cfac5f/final_image/MALAT1_fold_1.svg', '-title', 'MALAT1, -28.1 ± 1.1\n kcal/mol, AUC: 0.791', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,4,5,6,7,9,10,12,14,15,17,20,22,27,30,31,35,36,37,38,39,44,45,51,52,53,57,59,61,62,63,64,65,66,67,68,69,75,78,79,80,82,83,84,86,87,91,93,94,95,96,97,98,99,100,101,102,104,105,106,110,111', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '32,33,70,40,41,42,46,47,112,25', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,8,72,76,77,16,81,18,19,85,24,28,34,43,107,108,48,54', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '71,73,74,11,13,21,23,88,89,26,90,92,29,103,109,49,50,113,55,56,58,60']
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Text: '60', X: 169.82999811653394, Y: 168.3310550227845, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 101.45775449031362, Y: 312.98608905438766, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 162.79856876981862, Y: 201.45837555475578, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '90', X: 199.9933514840032, Y: 16.76913158111057, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '100', X: 249.59510629440706, Y: 177.27945778977247, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '110', X: 255.31561886658267, Y: 318.84395343065677, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '113', X: 307.81561886658267, Y: 318.84395343065677, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'MALAT1, -28.1 ± 1.1
 kcal/mol, AUC: 0.791', X: 94.40780943329133, Y: 331.6439534306568, Width: 142.5, Height: 23
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Updated SVG: /disk1/www/rails/humanrnamap/public/result/6c2b6901-a6c6-4213-9eca-6a9f41cfac5f/final_image/MALAT1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/6c2b6901-a6c6-4213-9eca-6a9f41cfac5f/final_image/MALAT1_fold_final_1.svg
