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/d4e095c5-e183-4663-bf10-c777c9a1fc15/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: 0.55 seconds
write fasta - Current memory usage: 172.16 MB
Length of region: 109 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/d4e095c5-e183-4663-bf10-c777c9a1fc15/fasta/MALAT1.fasta" "/disk1/www/rails/humanrnamap/public/result/d4e095c5-e183-4663-bf10-c777c9a1fc15/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/d4e095c5-e183-4663-bf10-c777c9a1fc15/ct/MALAT1.ct" "/disk1/www/rails/humanrnamap/public/result/d4e095c5-e183-4663-bf10-c777c9a1fc15/fold_FE/MALAT1.txt" -sh "MALAT1.dat"

efn2 - Elapsed time since the previous call: 0.42 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/d4e095c5-e183-4663-bf10-c777c9a1fc15/ct/MALAT1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/d4e095c5-e183-4663-bf10-c777c9a1fc15/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', 'AGGGCAGACUGCCAAGUCCUGGAGAAAUAGUAGAUGGCAAGUUUGUGGGUUUUUUUUUUUUACACGAAUUUGAGGAAAACCAAAUGAAUUUGAUAGCCAAAUUGAGACA', '-structureDBN', '...(((((((((((....(((......)))....)))).))))))).((((((((((..............)))))))))).....((((((.....))))))......', '-o', '/disk1/www/rails/humanrnamap/public/result/d4e095c5-e183-4663-bf10-c777c9a1fc15/final_image/MALAT1_fold_1.svg', '-title', 'MALAT1, -21.7 ± 1.0\n kcal/mol, AUC: 0.587', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,4,7,10,11,16,17,20,21,22,24,28,30,31,33,35,36,37,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,66,69,70,71,72,74,75,85,86,89,90,91,92,94,96,102,103,104,106', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '82,99', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,73,12,13,14,76,77,78,18,19,23,25,29,95,32,39,40,62', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,65,67,68,5,6,8,9,15,79,80,81,83,84,87,88,26,27,93,97,34,98,100,101,38,105,107,108,109,63']
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Warning: Font Verdana not found. Using default font.
Text: 'MALAT1, -21.7 ± 1.0
 kcal/mol, AUC: 0.587', X: 157.71037520189077, Y: 387.19138016045076, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 461.42075040378154, 387.19138016045076)
Updated viewBox: -0.25 0.0 466.67075040378154 392.19138016045076
Updated SVG: /disk1/www/rails/humanrnamap/public/result/d4e095c5-e183-4663-bf10-c777c9a1fc15/final_image/MALAT1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/d4e095c5-e183-4663-bf10-c777c9a1fc15/final_image/MALAT1_fold_final_1.svg
