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/1cb43449-f37d-42ff-b79d-c4c7c7a6b1e2/final_image/FOXRED2_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.30 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.30 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.30 MB
read annotations - Elapsed time since the previous call: 0.10 seconds
read annotations - Current memory usage: 172.96 MB
Based on canonical annotations, the following gene is in your area of interest: FOXRED2(-)
write fasta - Elapsed time since the previous call: 0.31 seconds
write fasta - Current memory usage: 172.96 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: 0.21 seconds
write dat - Current memory usage: 176.54 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/1cb43449-f37d-42ff-b79d-c4c7c7a6b1e2/fasta/FOXRED2.fasta" "/disk1/www/rails/humanrnamap/public/result/1cb43449-f37d-42ff-b79d-c4c7c7a6b1e2/ct/FOXRED2.ct" --SHAPE "FOXRED2.dat"

fold - Elapsed time since the previous call: 0.11 seconds
fold - Current memory usage: 176.54 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/1cb43449-f37d-42ff-b79d-c4c7c7a6b1e2/ct/FOXRED2.ct" "/disk1/www/rails/humanrnamap/public/result/1cb43449-f37d-42ff-b79d-c4c7c7a6b1e2/fold_FE/FOXRED2.txt" -sh "FOXRED2.dat"

efn2 - Elapsed time since the previous call: 0.43 seconds
efn2 - Current memory usage: 176.54 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/1cb43449-f37d-42ff-b79d-c4c7c7a6b1e2/ct/FOXRED2.ct" 1 "/disk1/www/rails/humanrnamap/public/result/1cb43449-f37d-42ff-b79d-c4c7c7a6b1e2/fold_dbn/FOXRED2_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.54 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CAGGCUGGAGUGCAAUGGCACGAUGUCGGCUCACUGCAACUUCUGCCUCCCGGGUCUAAACAAUUCUCUUCCCUCAACCUCCCAAGUAGC', '-structureDBN', '.((((.((((((((.((((.((....)))).)).)))).)))).))))...(((..........................))).......', '-o', '/disk1/www/rails/humanrnamap/public/result/1cb43449-f37d-42ff-b79d-c4c7c7a6b1e2/final_image/FOXRED2_fold_1.svg', '-title', 'FOXRED2, -34.7 ± 0.8\n kcal/mol, AUC: 0.705', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,4,6,7,8,10,11,12,16,17,18,22,24,25,26,28,29,31,35,36,41,42,44,45,48,52,53,54,55,57,64,65,67,69,70,74,80,86,87,89', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '2,5,9,13,14,19,20,21,23,27,30,32,33,34,37,40,43,46,47,49,50,51,56,58,60,63,68,72,73,75,76,77,79,81,82,83,88,90', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,66,84,38,39,62,78', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '85,71,59,61,15']
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Text: 'FOXRED2, -34.7 ± 0.8
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Calculated bounding box: (2.239550835758447, 5.0, 386.2242375307292, 429.6914858986962)
Updated viewBox: -2.760449164241553 0.0 393.9846866949708 434.6914858986962
Updated SVG: /disk1/www/rails/humanrnamap/public/result/1cb43449-f37d-42ff-b79d-c4c7c7a6b1e2/final_image/FOXRED2_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/1cb43449-f37d-42ff-b79d-c4c7c7a6b1e2/final_image/FOXRED2_fold_final_1.svg
