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/caad5dcd-2081-4716-88a5-8839f54ae413/final_image/HCFC1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.94 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.94 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.94 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.65 MB
Based on canonical annotations, the following gene is in your area of interest: HCFC1(-)
write fasta - Elapsed time since the previous call: 0.51 seconds
write fasta - Current memory usage: 172.65 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: 0.21 seconds
write dat - Current memory usage: 176.23 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/caad5dcd-2081-4716-88a5-8839f54ae413/fasta/HCFC1.fasta" "/disk1/www/rails/humanrnamap/public/result/caad5dcd-2081-4716-88a5-8839f54ae413/ct/HCFC1.ct" --SHAPE "HCFC1.dat"

fold - Elapsed time since the previous call: 0.15 seconds
fold - Current memory usage: 176.23 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/caad5dcd-2081-4716-88a5-8839f54ae413/ct/HCFC1.ct" "/disk1/www/rails/humanrnamap/public/result/caad5dcd-2081-4716-88a5-8839f54ae413/fold_FE/HCFC1.txt" -sh "HCFC1.dat"

efn2 - Elapsed time since the previous call: 0.53 seconds
efn2 - Current memory usage: 176.23 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/caad5dcd-2081-4716-88a5-8839f54ae413/ct/HCFC1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/caad5dcd-2081-4716-88a5-8839f54ae413/fold_dbn/HCFC1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 176.23 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CCGGGGGCCCUUCAGCGAAAUCUCAGCCUUUAAGACGUGCCUGCCUGGUUUCCCAGGGGCCCCUUGUGCCAUUAAAAUCAGCAAAAGUCCGGAUGGUGC', '-structureDBN', '..((((((((((....((((((.((((...........).)))...))))))..)))))))))).((((((((..................))))))))', '-o', '/disk1/www/rails/humanrnamap/public/result/caad5dcd-2081-4716-88a5-8839f54ae413/final_image/HCFC1_fold_1.svg', '-title', 'HCFC1, -35.1 ± 1.0\n kcal/mol, AUC: 0.709', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,4,5,6,7,11,12,15,17,21,23,26,29,30,31,34,37,38,39,42,43,46,47,48,49,50,51,56,57,58,59,64,65,66,67,68,72,73,78,81,87,88,91,92,94,95,96,97,98', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '1,99,10,75,79,93,89,90,60,61', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '2,69,71,8,9,76,18,19,25,40,41,45,52,53,55,62,63', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '70,74,13,14,77,16,80,82,83,20,84,22,85,24,86,27,28,32,33,35,36,44,54']
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Text: 'HCFC1, -35.1 ± 1.0
 kcal/mol, AUC: 0.709', X: 27.20106461591925, Y: 543.9687844219835, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 198.3527751803535, 543.9687844219835)
Updated viewBox: -0.25 0.0 203.6027751803535 548.9687844219835
Updated SVG: /disk1/www/rails/humanrnamap/public/result/caad5dcd-2081-4716-88a5-8839f54ae413/final_image/HCFC1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/caad5dcd-2081-4716-88a5-8839f54ae413/final_image/HCFC1_fold_final_1.svg
