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/600614bf-313a-4c08-8bfe-a772ff5e3e81/final_image/MALAT1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.80 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.80 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.80 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.35 MB
Based on canonical annotations, the following gene is in your area of interest: MALAT1(+)
write fasta - Elapsed time since the previous call: 0.63 seconds
write fasta - Current memory usage: 172.35 MB
Length of region: 86 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: 0.20 seconds
write dat - Current memory usage: 175.86 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/600614bf-313a-4c08-8bfe-a772ff5e3e81/fasta/MALAT1.fasta" "/disk1/www/rails/humanrnamap/public/result/600614bf-313a-4c08-8bfe-a772ff5e3e81/ct/MALAT1.ct" --SHAPE "MALAT1.dat"

fold - Elapsed time since the previous call: 0.14 seconds
fold - Current memory usage: 175.86 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/600614bf-313a-4c08-8bfe-a772ff5e3e81/ct/MALAT1.ct" "/disk1/www/rails/humanrnamap/public/result/600614bf-313a-4c08-8bfe-a772ff5e3e81/fold_FE/MALAT1.txt" -sh "MALAT1.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 175.86 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/600614bf-313a-4c08-8bfe-a772ff5e3e81/ct/MALAT1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/600614bf-313a-4c08-8bfe-a772ff5e3e81/fold_dbn/MALAT1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 175.86 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AGAGAAAGGACUACAGAGCCCCGAAUUAAUACCAAUAGAAGGGCAAUGCUUUUAGAUUAAAAUGAAGGUGACUUAAACAGCUUAAA', '-structureDBN', '.............((..((((...................))))..))((((((........))))))..................', '-o', '/disk1/www/rails/humanrnamap/public/result/600614bf-313a-4c08-8bfe-a772ff5e3e81/final_image/MALAT1_fold_1.svg', '-title', 'MALAT1, -11.1 ± 0.7\n kcal/mol, AUC: 0.655', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,4,8,9,12,16,18,23,26,27,30,36,38,41,42,43,47,48,50,51,52,53,55,57,58,63,64,67,68,69,70,73,74,80,82,83', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '19,20,21,54,59,60', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '66,7,75,15,79,84,22,86,28,29', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,3,5,6,10,11,13,14,17,24,25,31,32,33,34,35,37,39,40,44,45,46,49,56,61,62,65,71,72,76,77,78,81,85']
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Text: 'G', X: 264.75, Y: 270.4183836512484, Width: 10.5, Height: 8
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Text: 'U', X: 282.25, Y: 250.41838365124838, Width: 10.5, Height: 8
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Text: 'U', X: 282.25, Y: 230.41838365124838, Width: 10.5, Height: 8
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Text: 'U', X: 314.75, Y: 170.41838365124838, Width: 10.5, Height: 8
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Text: 'G', X: 314.75, Y: 190.41838365124838, Width: 10.5, Height: 8
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Text: 'A', X: 314.75, Y: 230.41838365124838, Width: 10.5, Height: 8
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Text: 'G', X: 314.75, Y: 250.41838365124838, Width: 10.5, Height: 8
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Text: 'G', X: 314.75, Y: 270.4183836512484, Width: 10.5, Height: 8
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Text: 'U', X: 332.25, Y: 270.4183836512484, Width: 10.5, Height: 8
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Text: 'G', X: 349.75, Y: 270.4183836512484, Width: 10.5, Height: 8
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Text: 'A', X: 367.25, Y: 270.4183836512484, Width: 10.5, Height: 8
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Text: 'C', X: 384.75, Y: 270.4183836512484, Width: 10.5, Height: 8
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Text: 'U', X: 402.25, Y: 270.4183836512484, Width: 10.5, Height: 8
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Text: 'U', X: 419.75, Y: 270.4183836512484, Width: 10.5, Height: 8
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Text: 'A', X: 437.25, Y: 270.4183836512484, Width: 10.5, Height: 8
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Text: 'A', X: 507.25, Y: 270.4183836512484, Width: 10.5, Height: 8
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Text: 'C', X: 542.25, Y: 270.4183836512484, Width: 10.5, Height: 8
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Text: 'A', X: 629.75, Y: 270.4183836512484, Width: 10.5, Height: 8
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Text: '10', X: 158.5, Y: 290.4183836512484, Width: 18.0, Height: 8
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Text: '20', X: 208.5, Y: 164.73950168511527, Width: 18.0, Height: 8
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Text: '30', X: 221.763827648477, Y: 8.0, Width: 18.0, Height: 8
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Text: '40', X: 287.59192009126076, Y: 154.70504738862334, Width: 18.0, Height: 8
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Text: '50', X: 258.5, Y: 250.41838365124838, Width: 18.0, Height: 8
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Text: '86', X: 626.0, Y: 290.4183836512484, Width: 18.0, Height: 8
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Text: 'MALAT1, -11.1 ± 0.7
 kcal/mol, AUC: 0.655', X: 251.25, Y: 303.2183836512484, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 644.0, 303.2183836512484)
Updated viewBox: -0.25 -5.0 649.25 313.2183836512484
Updated SVG: /disk1/www/rails/humanrnamap/public/result/600614bf-313a-4c08-8bfe-a772ff5e3e81/final_image/MALAT1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/600614bf-313a-4c08-8bfe-a772ff5e3e81/final_image/MALAT1_fold_final_1.svg
