Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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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/6f5fe12d-e1d7-4830-8a5e-f47b3a64f0da/final_image/IDS_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.27 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.27 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.27 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.96 MB
Based on canonical annotations, the following gene is in your area of interest: IDS(-)
write fasta - Elapsed time since the previous call: 0.28 seconds
write fasta - Current memory usage: 172.96 MB
Length of region: 102 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: 0.20 seconds
write dat - Current memory usage: 176.45 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/6f5fe12d-e1d7-4830-8a5e-f47b3a64f0da/fasta/IDS.fasta" "/disk1/www/rails/humanrnamap/public/result/6f5fe12d-e1d7-4830-8a5e-f47b3a64f0da/ct/IDS.ct" --SHAPE "IDS.dat"

fold - Elapsed time since the previous call: 0.13 seconds
fold - Current memory usage: 176.45 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/6f5fe12d-e1d7-4830-8a5e-f47b3a64f0da/ct/IDS.ct" "/disk1/www/rails/humanrnamap/public/result/6f5fe12d-e1d7-4830-8a5e-f47b3a64f0da/fold_FE/IDS.txt" -sh "IDS.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 176.45 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/6f5fe12d-e1d7-4830-8a5e-f47b3a64f0da/ct/IDS.ct" 1 "/disk1/www/rails/humanrnamap/public/result/6f5fe12d-e1d7-4830-8a5e-f47b3a64f0da/fold_dbn/IDS_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 176.45 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CCGCCAGAGCUACUUUGCCUCUGUGUCAUAUUUGGAUACACAGGUCGGCCGCCUCUUGAGUGCUUUGGACGAUCUUCAGCUGGCCAACAGCACCAUCAUUGC', '-structureDBN', '.(((((((((.((((.((((.((((((.......)))))).)))).((...))....))))))))))).)).......((((.....))))...........', '-o', '/disk1/www/rails/humanrnamap/public/result/6f5fe12d-e1d7-4830-8a5e-f47b3a64f0da/final_image/IDS_fold_1.svg', '-title', 'IDS, -28.6 ± 0.8\n kcal/mol, AUC: 0.592', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,7,9,11,14,15,16,17,20,22,23,24,25,26,29,31,32,33,34,35,37,43,44,45,47,48,51,54,56,57,58,60,61,62,64,65,66,67,68,71,73,75,76,79,81,82,83,90,96,99,100,101', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '1,2,4,69,70,42,74,77,49,19,94,63', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '5,8,10,21,85,88,89,27,97,36,39,40,41,46,50,52,59', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '6,72,12,13,78,80,18,84,86,87,91,28,92,30,93,95,98,38,102,53,55']
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Text: 'IDS, -28.6 ± 0.8
 kcal/mol, AUC: 0.592', X: 306.6762451018589, Y: 417.1782804890835, Width: 142.5, Height: 23
Calculated bounding box: (-4.0, 0.0, 753.6475141141369, 417.1782804890835)
Updated viewBox: -9.0 -5.0 767.6475141141369 427.1782804890835
Updated SVG: /disk1/www/rails/humanrnamap/public/result/6f5fe12d-e1d7-4830-8a5e-f47b3a64f0da/final_image/IDS_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/6f5fe12d-e1d7-4830-8a5e-f47b3a64f0da/final_image/IDS_fold_final_1.svg
