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/36af908d-bffb-41ed-a670-ca4100d095a7/final_image/MALAT1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.63 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.63 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.63 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.16 MB
Based on canonical annotations, the following gene is in your area of interest: MALAT1(+)
write fasta - Elapsed time since the previous call: 0.57 seconds
write fasta - Current memory usage: 172.16 MB
Length of region: 124 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: 0.18 seconds
write dat - Current memory usage: 175.70 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/36af908d-bffb-41ed-a670-ca4100d095a7/fasta/MALAT1.fasta" "/disk1/www/rails/humanrnamap/public/result/36af908d-bffb-41ed-a670-ca4100d095a7/ct/MALAT1.ct" --SHAPE "MALAT1.dat"

fold - Elapsed time since the previous call: 0.19 seconds
fold - Current memory usage: 175.70 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/36af908d-bffb-41ed-a670-ca4100d095a7/ct/MALAT1.ct" "/disk1/www/rails/humanrnamap/public/result/36af908d-bffb-41ed-a670-ca4100d095a7/fold_FE/MALAT1.txt" -sh "MALAT1.dat"

efn2 - Elapsed time since the previous call: 0.51 seconds
efn2 - Current memory usage: 175.70 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/36af908d-bffb-41ed-a670-ca4100d095a7/ct/MALAT1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/36af908d-bffb-41ed-a670-ca4100d095a7/fold_dbn/MALAT1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.70 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AGGAAAGUGUCAUAAUUUGAUACUGUAUCUGUUUUCCUUCAAAGUAUAGAGCUUUUGGGGAAGGAAAGUAUUGAACUGGGGGUUGGUCUGGCCUACUGGGCUGACAUUAACUACAAUUAUGGGA', '-structureDBN', '.(((.(((((((.....)))))))...))).((((((((((((((.....)))))....)))))))))............((((((((.(((((...))))))))..)))))............', '-o', '/disk1/www/rails/humanrnamap/public/result/36af908d-bffb-41ed-a670-ca4100d095a7/final_image/MALAT1_fold_1.svg', '-title', 'MALAT1, -35.1 ± 2.0\n kcal/mol, AUC: 0.839', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,7,8,9,10,13,16,17,18,19,21,24,25,26,28,30,31,32,33,34,35,38,39,44,45,47,49,51,53,54,55,56,57,58,59,60,63,64,68,69,71,72,73,77,78,79,80,81,82,83,84,85,86,87,89,90,91,94,97,98,99,100,102,103,107,108,112,117,118,120,121,122,123', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '36,37,6,101,11,20,22,23,92,93,62', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,65,66,4,67,12,88,40,104,42,43,105,109,110,48,124,61', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '5,70,74,75,76,14,15,27,29,95,96,41,106,46,111,113,50,114,52,115,116,119']
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Warning: Font Verdana not found. Using default font.
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Warning: Font Verdana not found. Using default font.
Text: 'G', X: 657.925640773168, Y: 269.3351560619953, Width: 10.5, Height: 8
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Text: 'A', X: 675.425640773168, Y: 269.3351560619953, Width: 10.5, Height: 8
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Text: '1', X: 88.67564077316803, Y: 289.33515606199524, Width: 9.0, Height: 8
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Text: '124', X: 667.175640773168, Y: 289.3351560619953, Width: 27.0, Height: 8
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Text: 'MALAT1, -35.1 ± 2.0
 kcal/mol, AUC: 0.839', X: 274.087820386584, Y: 302.1351560619953, Width: 142.5, Height: 23
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Updated SVG: /disk1/www/rails/humanrnamap/public/result/36af908d-bffb-41ed-a670-ca4100d095a7/final_image/MALAT1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/36af908d-bffb-41ed-a670-ca4100d095a7/final_image/MALAT1_fold_final_1.svg
