Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 98% [==================================================] \                     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/54347c92-6d50-4f3f-9773-6ecef6f96fb9/final_image/CALD1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.00 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.00 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.00 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 171.50 MB
Based on canonical annotations, the following gene is in your area of interest: CALD1(+)
write fasta - Elapsed time since the previous call: 0.82 seconds
write fasta - Current memory usage: 171.50 MB
Length of region: 91 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: 174.98 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/54347c92-6d50-4f3f-9773-6ecef6f96fb9/fasta/CALD1.fasta" "/disk1/www/rails/humanrnamap/public/result/54347c92-6d50-4f3f-9773-6ecef6f96fb9/ct/CALD1.ct" --SHAPE "CALD1.dat"

fold - Elapsed time since the previous call: 0.10 seconds
fold - Current memory usage: 174.98 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/54347c92-6d50-4f3f-9773-6ecef6f96fb9/ct/CALD1.ct" "/disk1/www/rails/humanrnamap/public/result/54347c92-6d50-4f3f-9773-6ecef6f96fb9/fold_FE/CALD1.txt" -sh "CALD1.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 174.98 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/54347c92-6d50-4f3f-9773-6ecef6f96fb9/ct/CALD1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/54347c92-6d50-4f3f-9773-6ecef6f96fb9/fold_dbn/CALD1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 174.98 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AGUUAAGUCGCAGAAUGGAGAAUUCAUGACCCACAAACUUAAACAUACUGAGAAUACUUUCAGCCGCCCUGGAGGGAGGGCCAGCGUGGAC', '-structureDBN', '......((((..((((.....)))).))))((((.............((((((....))))))..(((((......)))))....))))..', '-o', '/disk1/www/rails/humanrnamap/public/result/54347c92-6d50-4f3f-9773-6ecef6f96fb9/final_image/CALD1_fold_1.svg', '-title', 'CALD1, -18.2 ± 0.8\n kcal/mol, AUC: 0.545', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,4,7,8,10,13,16,17,18,20,23,24,27,28,39,40,46,49,50,52,55,58,59,60,63,66,70,71,72,74,75,76,78,79,80,84,86,87,88,89', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '64,81,67,68,69,91', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '65,5,6,73,77,82,19,83,85,25,29,31,33,36,37,41,45,54,61,62', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,9,11,12,14,15,21,22,26,90,30,32,34,35,38,42,43,44,47,48,51,53,56,57']
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Text: 'CALD1, -18.2 ± 0.8
 kcal/mol, AUC: 0.545', X: 123.8411479942254, Y: 369.3570038459649, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 385.4322959884508, 369.3570038459649)
Updated viewBox: -0.25 0.0 390.6822959884508 374.3570038459649
Updated SVG: /disk1/www/rails/humanrnamap/public/result/54347c92-6d50-4f3f-9773-6ecef6f96fb9/final_image/CALD1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/54347c92-6d50-4f3f-9773-6ecef6f96fb9/final_image/CALD1_fold_final_1.svg
