Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 95% [================================================  ] |                     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/703cf565-40d4-42eb-8cb6-b1057e7b6253/final_image/MALAT1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.46 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.46 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.46 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 171.98 MB
Based on canonical annotations, the following gene is in your area of interest: MALAT1(+)
write fasta - Elapsed time since the previous call: 0.54 seconds
write fasta - Current memory usage: 171.98 MB
Length of region: 99 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: 0.24 seconds
write dat - Current memory usage: 175.63 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/703cf565-40d4-42eb-8cb6-b1057e7b6253/fasta/MALAT1.fasta" "/disk1/www/rails/humanrnamap/public/result/703cf565-40d4-42eb-8cb6-b1057e7b6253/ct/MALAT1.ct" --SHAPE "MALAT1.dat"

fold - Elapsed time since the previous call: 0.14 seconds
fold - Current memory usage: 175.63 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/703cf565-40d4-42eb-8cb6-b1057e7b6253/ct/MALAT1.ct" "/disk1/www/rails/humanrnamap/public/result/703cf565-40d4-42eb-8cb6-b1057e7b6253/fold_FE/MALAT1.txt" -sh "MALAT1.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 175.63 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/703cf565-40d4-42eb-8cb6-b1057e7b6253/ct/MALAT1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/703cf565-40d4-42eb-8cb6-b1057e7b6253/fold_dbn/MALAT1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 175.63 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CAGAUGUUACUGCUAAAAUUUACAUGUUGUGAUGUAAAUUGUGUAGAAAACCAUUAAAUCAUUCAAAAUAAUAAACUAUUUUUAUUAGAGAAUGUAUAC', '-structureDBN', '..((((((.((((...(((((((((......)))))))))..))))..)).))))....(((((....(((((((.....)))))))..))))).....', '-o', '/disk1/www/rails/humanrnamap/public/result/703cf565-40d4-42eb-8cb6-b1057e7b6253/final_image/MALAT1_fold_1.svg', '-title', 'MALAT1, -16.8 ± 1.3\n kcal/mol, AUC: 0.578', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,5,6,7,8,11,12,14,19,20,21,25,26,27,28,29,30,31,33,34,35,39,40,41,42,43,44,46,54,55,59,62,63,69,72,77,79,80,81,82,83,85,86,88,90,93,94,95,97', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '36,37,45,78,15,16,22,87,24', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '65,2,66,70,71,73,74,17,18,84,23,32,38,48,49,56,57', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,1,67,4,68,9,10,75,76,13,89,91,92,96,98,99,47,50,51,52,53,58,60,61']
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Text: 'MALAT1, -16.8 ± 1.3
 kcal/mol, AUC: 0.578', X: 161.8003369736747, Y: 454.84081001669307, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 479.9916778045242, 454.84081001669307)
Updated viewBox: -0.25 -5.0 485.2416778045242 464.84081001669307
Updated SVG: /disk1/www/rails/humanrnamap/public/result/703cf565-40d4-42eb-8cb6-b1057e7b6253/final_image/MALAT1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/703cf565-40d4-42eb-8cb6-b1057e7b6253/final_image/MALAT1_fold_final_1.svg
