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/abe7dc20-b651-4f69-a518-c54816ee94fb/final_image/CHD2_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.86 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.86 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.86 MB
read annotations - Elapsed time since the previous call: 0.10 seconds
read annotations - Current memory usage: 172.48 MB
Based on canonical annotations, the following gene is in your area of interest: CHD2(+)
write fasta - Elapsed time since the previous call: 0.33 seconds
write fasta - Current memory usage: 172.48 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: 0.18 seconds
write dat - Current memory usage: 176.05 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/abe7dc20-b651-4f69-a518-c54816ee94fb/fasta/CHD2.fasta" "/disk1/www/rails/humanrnamap/public/result/abe7dc20-b651-4f69-a518-c54816ee94fb/ct/CHD2.ct" --SHAPE "CHD2.dat"

fold - Elapsed time since the previous call: 0.12 seconds
fold - Current memory usage: 176.05 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/abe7dc20-b651-4f69-a518-c54816ee94fb/ct/CHD2.ct" "/disk1/www/rails/humanrnamap/public/result/abe7dc20-b651-4f69-a518-c54816ee94fb/fold_FE/CHD2.txt" -sh "CHD2.dat"

efn2 - Elapsed time since the previous call: 0.52 seconds
efn2 - Current memory usage: 176.05 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/abe7dc20-b651-4f69-a518-c54816ee94fb/ct/CHD2.ct" 1 "/disk1/www/rails/humanrnamap/public/result/abe7dc20-b651-4f69-a518-c54816ee94fb/fold_dbn/CHD2_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.05 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AGCUUUAAAGAAACAACCUGCAUAUUUAGGAGGGGAGAAUCUGGAACUUCGAGAUUAUCAGCUAGAAGGUCUAAACUGGCUAGCUCAUUCCUGGUGCAA', '-structureDBN', '..................(((((...((((((..((..((((.((...)).))))..)).(((((..(((....)))..)))))...))))))))))).', '-o', '/disk1/www/rails/humanrnamap/public/result/abe7dc20-b651-4f69-a518-c54816ee94fb/final_image/CHD2_fold_1.svg', '-title', 'CHD2, -17.0 ± 1.3\n kcal/mol, AUC: 0.622', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,4,5,6,10,19,20,23,25,26,27,29,30,32,33,34,35,37,40,42,43,44,48,49,51,53,55,56,58,61,63,65,68,69,70,72,77,78,79,81,83,85,88,89,92,93,94,95,96', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '98,91', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,97,67,7,41,73,11,18,84,87,57,31', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '3,8,9,12,13,14,15,16,17,21,22,24,28,36,38,39,45,46,47,50,52,54,59,60,62,64,66,71,74,75,76,80,82,86,90,99']
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Text: 'CHD2, -17.0 ± 1.3
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Calculated bounding box: (4.75, 5.0, 717.5939296562698, 465.0946051972321)
Updated viewBox: -0.25 0.0 722.8439296562698 470.0946051972321
Updated SVG: /disk1/www/rails/humanrnamap/public/result/abe7dc20-b651-4f69-a518-c54816ee94fb/final_image/CHD2_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/abe7dc20-b651-4f69-a518-c54816ee94fb/final_image/CHD2_fold_final_1.svg
