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/eb41b936-be0d-431f-9c9c-1f09cdafce5c/final_image/ITCH_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.23 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.23 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.23 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.89 MB
Based on canonical annotations, the following gene is in your area of interest: ITCH(+)
write fasta - Elapsed time since the previous call: 0.59 seconds
write fasta - Current memory usage: 172.89 MB
Length of region: 105 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: 176.46 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/eb41b936-be0d-431f-9c9c-1f09cdafce5c/fasta/ITCH.fasta" "/disk1/www/rails/humanrnamap/public/result/eb41b936-be0d-431f-9c9c-1f09cdafce5c/ct/ITCH.ct" --SHAPE "ITCH.dat"

fold - Elapsed time since the previous call: 0.13 seconds
fold - Current memory usage: 176.46 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/eb41b936-be0d-431f-9c9c-1f09cdafce5c/ct/ITCH.ct" "/disk1/www/rails/humanrnamap/public/result/eb41b936-be0d-431f-9c9c-1f09cdafce5c/fold_FE/ITCH.txt" -sh "ITCH.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 176.46 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/eb41b936-be0d-431f-9c9c-1f09cdafce5c/ct/ITCH.ct" 1 "/disk1/www/rails/humanrnamap/public/result/eb41b936-be0d-431f-9c9c-1f09cdafce5c/fold_dbn/ITCH_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.46 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CGUCAUUAUGCAAGGACCAGCAAACAAAUCAUGUGGUUUUGGCAGUUUGUUAAAGAAAUUGAUAAUGAGAAGAGAAUGAGACUUCUGCAGUUUGUUACUGGAACC', '-structureDBN', '...((...(((.(((((((.((.........))))))))).)))...))..................(((((.........))))).((((.....)))).....', '-o', '/disk1/www/rails/humanrnamap/public/result/eb41b936-be0d-431f-9c9c-1f09cdafce5c/final_image/ITCH_fold_1.svg', '-title', 'ITCH, -12.5 ± 0.9\n kcal/mol, AUC: 0.624', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,6,7,9,10,14,15,20,29,32,33,34,35,36,37,38,39,40,41,42,45,46,47,48,49,50,51,55,59,60,61,63,66,67,69,72,74,77,78,80,83,84,86,87,90,91,92,93,94,95,96,99,100,101', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '18,26,4,85,8,105,56', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '89,97,5,102,17,81,19,52,22,57,30', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,11,12,13,16,21,23,24,25,27,28,31,43,44,53,54,58,62,64,65,68,70,71,73,75,76,79,82,88,98,103,104']
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Text: '105', X: 601.5, Y: 405.72948271843603, Width: 27.0, Height: 8
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Text: 'ITCH, -12.5 ± 0.9
 kcal/mol, AUC: 0.624', X: 241.25, Y: 418.52948271843604, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 628.5, 418.52948271843604)
Updated viewBox: -0.25 0.0 633.75 423.52948271843604
Updated SVG: /disk1/www/rails/humanrnamap/public/result/eb41b936-be0d-431f-9c9c-1f09cdafce5c/final_image/ITCH_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/eb41b936-be0d-431f-9c9c-1f09cdafce5c/final_image/ITCH_fold_final_1.svg
