Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 97% [================================================= ] \                     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/ec81461d-73bc-415c-99e3-bcf0159e37db/final_image/MALAT1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.79 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.79 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.79 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.46 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: 172.46 MB
Length of region: 92 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: 0.16 seconds
write dat - Current memory usage: 175.59 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/ec81461d-73bc-415c-99e3-bcf0159e37db/fasta/MALAT1.fasta" "/disk1/www/rails/humanrnamap/public/result/ec81461d-73bc-415c-99e3-bcf0159e37db/ct/MALAT1.ct" --SHAPE "MALAT1.dat"

fold - Elapsed time since the previous call: 0.10 seconds
fold - Current memory usage: 175.59 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/ec81461d-73bc-415c-99e3-bcf0159e37db/ct/MALAT1.ct" "/disk1/www/rails/humanrnamap/public/result/ec81461d-73bc-415c-99e3-bcf0159e37db/fold_FE/MALAT1.txt" -sh "MALAT1.dat"

efn2 - Elapsed time since the previous call: 0.50 seconds
efn2 - Current memory usage: 175.59 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/ec81461d-73bc-415c-99e3-bcf0159e37db/ct/MALAT1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/ec81461d-73bc-415c-99e3-bcf0159e37db/fold_dbn/MALAT1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.59 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AAGAUGAGGGUGUUUACGUAGACCAGAACCAAUUUAGAAGAAUACUUGAAGCUAGAAGGGGAAGUUGGUUAAAAAUCACAUCAAAAAGCUAC', '-structureDBN', '....(((..(((......(((.((((..((..(((((..............)))))..))....))))))).....))).))).........', '-o', '/disk1/www/rails/humanrnamap/public/result/ec81461d-73bc-415c-99e3-bcf0159e37db/final_image/MALAT1_fold_1.svg', '-title', 'MALAT1, -8.4 ± 1.2\n kcal/mol, AUC: 0.554', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,5,6,8,9,10,11,12,13,14,15,18,19,21,26,33,34,35,37,40,43,46,47,48,51,53,55,58,59,60,61,64,65,66,67,68,69,70,76,81,88,90', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '83,87,71,89,91', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '2,7,73,50,82,20,84,54,86,24,25,92,63,62,31', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,4,72,74,75,77,78,79,16,17,80,85,22,23,27,28,29,30,32,36,38,39,41,42,44,45,49,52,56,57']
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Text: 'MALAT1, -8.4 ± 1.2
 kcal/mol, AUC: 0.554', X: 137.34394030450247, Y: 587.2070247434476, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 412.43788060900494, 587.2070247434476)
Updated viewBox: -0.25 0.0 417.68788060900494 592.2070247434476
Updated SVG: /disk1/www/rails/humanrnamap/public/result/ec81461d-73bc-415c-99e3-bcf0159e37db/final_image/MALAT1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/ec81461d-73bc-415c-99e3-bcf0159e37db/final_image/MALAT1_fold_final_1.svg
