Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 94% [================================================  ] -                     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/242ff432-5c3c-445f-acb5-cb5d0b652047/final_image/DNAJC13_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.93 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.93 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.93 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.45 MB
Based on canonical annotations, the following gene is in your area of interest: DNAJC13(+)
write fasta - Elapsed time since the previous call: 1.28 seconds
write fasta - Current memory usage: 172.45 MB
Length of region: 90 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: 176.00 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/242ff432-5c3c-445f-acb5-cb5d0b652047/fasta/DNAJC13.fasta" "/disk1/www/rails/humanrnamap/public/result/242ff432-5c3c-445f-acb5-cb5d0b652047/ct/DNAJC13.ct" --SHAPE "DNAJC13.dat"

fold - Elapsed time since the previous call: 0.10 seconds
fold - Current memory usage: 176.00 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/242ff432-5c3c-445f-acb5-cb5d0b652047/ct/DNAJC13.ct" "/disk1/www/rails/humanrnamap/public/result/242ff432-5c3c-445f-acb5-cb5d0b652047/fold_FE/DNAJC13.txt" -sh "DNAJC13.dat"

efn2 - Elapsed time since the previous call: 0.53 seconds
efn2 - Current memory usage: 176.00 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/242ff432-5c3c-445f-acb5-cb5d0b652047/ct/DNAJC13.ct" 1 "/disk1/www/rails/humanrnamap/public/result/242ff432-5c3c-445f-acb5-cb5d0b652047/fold_dbn/DNAJC13_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.00 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AAAGAAGCAAUGGCAAAGGGUGCUUUGAUCUAUUUACUGGAUAUGUUCUGCAAUUCAACACAUCCACAGGUUCGAGCCCAAACAGCAGAA', '-structureDBN', '............((....((.((((.(((((......(((((.((((.........)))).))))).))))).)))))).....))....', '-o', '/disk1/www/rails/humanrnamap/public/result/242ff432-5c3c-445f-acb5-cb5d0b652047/final_image/DNAJC13_fold_1.svg', '-title', 'DNAJC13, -22.4 ± 1.0\n kcal/mol, AUC: 0.815', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '4,7,11,12,13,18,19,20,21,22,24,25,26,27,29,31,33,34,35,38,39,40,42,44,45,46,47,49,50,54,55,63,69,70,71,72,74,76,85,88', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '1,65,77,14,15,78,79,80,86,23,90,28,41,43,56,58,59,60,61,62', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '64,89,66,68,8,73,16,48,17,51,84,87,57,30', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '2,3,67,5,6,9,10,75,81,82,83,32,36,37,52,53']
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Text: 'DNAJC13, -22.4 ± 1.0
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Calculated bounding box: (4.75, 0.0, 542.9661386840186, 426.3200756388756)
Updated viewBox: -0.25 -5.0 548.2161386840186 436.3200756388756
Updated SVG: /disk1/www/rails/humanrnamap/public/result/242ff432-5c3c-445f-acb5-cb5d0b652047/final_image/DNAJC13_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/242ff432-5c3c-445f-acb5-cb5d0b652047/final_image/DNAJC13_fold_final_1.svg
