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/d17445d6-5ca3-446e-952b-2b479e207bec/final_image/MALAT1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.50 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.50 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.50 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.02 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: 172.02 MB
Length of region: 112 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/d17445d6-5ca3-446e-952b-2b479e207bec/fasta/MALAT1.fasta" "/disk1/www/rails/humanrnamap/public/result/d17445d6-5ca3-446e-952b-2b479e207bec/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/d17445d6-5ca3-446e-952b-2b479e207bec/ct/MALAT1.ct" "/disk1/www/rails/humanrnamap/public/result/d17445d6-5ca3-446e-952b-2b479e207bec/fold_FE/MALAT1.txt" -sh "MALAT1.dat"

efn2 - Elapsed time since the previous call: 0.43 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/d17445d6-5ca3-446e-952b-2b479e207bec/ct/MALAT1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/d17445d6-5ca3-446e-952b-2b479e207bec/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', 'AGAACUUCAGAAGAGCUUGAGUAGGCCAAAUGUUGAAGUUAAGUUUUCCAAUAAUGUGACUUCUUAAAAGUUUUAUUAAAGGGGAGGGGCAAAUAUUGGCAAUUAGUUGGCA', '-structureDBN', '..............((.(((.((((((((.((((...(((...((((((..(((((.(((((.....))))).)))))..)))))).))).)))))))))..))).))))).', '-o', '/disk1/www/rails/humanrnamap/public/result/d17445d6-5ca3-446e-952b-2b479e207bec/final_image/MALAT1_fold_1.svg', '-title', 'MALAT1, -15.7 ± 1.4\n kcal/mol, AUC: 0.571', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,6,7,10,13,15,17,18,19,21,22,24,25,31,32,33,34,35,38,39,40,43,44,45,46,47,52,55,56,57,58,61,62,64,65,70,71,72,73,74,76,77,81,82,83,84,86,87,88,89,94,96,97,98,99,103,104,106,107,108,109,110', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '66,37,105,42,28,78', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,36,68,69,91,75,79,111,53,23,27', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '3,4,5,8,9,11,12,14,16,20,26,29,30,41,48,49,50,51,54,59,60,63,67,80,85,90,92,93,95,100,101,102,112']
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Text: '110', X: 294.0, Y: 553.7662915894373, Width: 27.0, Height: 8
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Text: '112', X: 291.5, Y: 593.7662915894373, Width: 27.0, Height: 8
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Text: 'MALAT1, -15.7 ± 1.4
 kcal/mol, AUC: 0.571', X: 297.46174087829587, Y: 606.5662915894372, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 732.6734817565917, 606.5662915894372)
Updated viewBox: -0.25 0.0 737.9234817565917 611.5662915894372
Updated SVG: /disk1/www/rails/humanrnamap/public/result/d17445d6-5ca3-446e-952b-2b479e207bec/final_image/MALAT1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/d17445d6-5ca3-446e-952b-2b479e207bec/final_image/MALAT1_fold_final_1.svg
