Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
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 90% [==============================================    ] |                     
 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/ed05cac9-e983-4843-9ac3-aa18cb24c646/final_image/LMNA_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 156.70 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 156.70 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 156.70 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 170.23 MB
Based on canonical annotations, the following gene is in your area of interest: LMNA(+)
write fasta - Elapsed time since the previous call: 0.98 seconds
write fasta - Current memory usage: 170.23 MB
Length of region: 83 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: 173.49 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/ed05cac9-e983-4843-9ac3-aa18cb24c646/fasta/LMNA.fasta" "/disk1/www/rails/humanrnamap/public/result/ed05cac9-e983-4843-9ac3-aa18cb24c646/ct/LMNA.ct" --SHAPE "LMNA.dat"

fold - Elapsed time since the previous call: 0.09 seconds
fold - Current memory usage: 173.49 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/ed05cac9-e983-4843-9ac3-aa18cb24c646/ct/LMNA.ct" "/disk1/www/rails/humanrnamap/public/result/ed05cac9-e983-4843-9ac3-aa18cb24c646/fold_FE/LMNA.txt" -sh "LMNA.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 173.49 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/ed05cac9-e983-4843-9ac3-aa18cb24c646/ct/LMNA.ct" 1 "/disk1/www/rails/humanrnamap/public/result/ed05cac9-e983-4843-9ac3-aa18cb24c646/fold_dbn/LMNA_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 173.49 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CUGCCAGGAGCAAGCCGAGAGCCAGCCGGCCGGCGCACUCCGACUCCGAGCAGUCUCUGUCCUUCGACCCGAGCCCCGCGCCC', '-structureDBN', '((((..((((...((((...(((....))))))).........))))..)))).(((.(((....)))..)))..........', '-o', '/disk1/www/rails/humanrnamap/public/result/ed05cac9-e983-4843-9ac3-aa18cb24c646/final_image/LMNA_fold_1.svg', '-title', 'LMNA, -22.1 ± 1.3\n kcal/mol, AUC: 0.678', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,7,8,10,14,17,19,21,25,28,29,32,33,35,39,42,45,48,50,53,54,56,58,59,60,63,64,66,71,73,78,80', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '1,82,83,23,31,30,15', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '34,40,9,41,11,12,44,75,76,16,81,22,55,27', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '65,67,4,5,6,68,69,70,72,74,13,77,79,18,20,24,26,36,37,38,43,46,47,49,51,52,57,61,62']
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Text: 'U', X: 171.24369416336557, Y: 232.0429116248874, Width: 10.5, Height: 8
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Text: 'A', X: 171.24369416336557, Y: 357.7217935910205, Width: 10.5, Height: 8
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Text: 'G', X: 171.24369416336557, Y: 377.7217935910205, Width: 10.5, Height: 8
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Text: 'U', X: 188.74369416336557, Y: 377.7217935910205, Width: 10.5, Height: 8
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Text: 'C', X: 206.24369416336557, Y: 377.7217935910205, Width: 10.5, Height: 8
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Text: 'U', X: 206.24369416336557, Y: 357.7217935910205, Width: 10.5, Height: 8
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Text: 'C', X: 206.24369416336557, Y: 337.7217935910205, Width: 10.5, Height: 8
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Text: 'U', X: 193.62375907300375, Y: 286.58324972246, Width: 10.5, Height: 8
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Text: 'C', X: 244.48407521848492, Y: 305.3626993703191, Width: 10.5, Height: 8
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Text: 'C', X: 247.54083832205643, Y: 322.593665661524, Width: 10.5, Height: 8
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Text: 'G', X: 238.74369416336557, Y: 337.7217935910205, Width: 10.5, Height: 8
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Text: 'A', X: 238.74369416336557, Y: 357.7217935910205, Width: 10.5, Height: 8
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Text: 'G', X: 238.74369416336557, Y: 377.7217935910205, Width: 10.5, Height: 8
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Text: '10', X: 116.91682534933409, Y: 220.6001783544159, Width: 18.0, Height: 8
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Text: '20', X: -4.0, Y: 95.42824420012727, Width: 18.0, Height: 8
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Text: '70', X: 263.4833819947079, Y: 326.08704850637764, Width: 18.0, Height: 8
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Text: '83', X: 409.9936941633656, Y: 397.72179359102057, Width: 18.0, Height: 8
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Text: 'LMNA, -22.1 ± 1.3
 kcal/mol, AUC: 0.678', X: 150.59645258974265, Y: 410.5217935910206, Width: 142.5, Height: 23
Calculated bounding box: (-4.0, 5.0, 427.9936941633656, 410.5217935910206)
Updated viewBox: -9.0 0.0 441.9936941633656 415.5217935910206
Updated SVG: /disk1/www/rails/humanrnamap/public/result/ed05cac9-e983-4843-9ac3-aa18cb24c646/final_image/LMNA_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/ed05cac9-e983-4843-9ac3-aa18cb24c646/final_image/LMNA_fold_final_1.svg
