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/16fa5ed2-95c8-449c-aae9-7c74bbdcabfd/final_image/HCFC1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.78 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.78 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.78 MB
read annotations - Elapsed time since the previous call: 0.10 seconds
read annotations - Current memory usage: 172.39 MB
Based on canonical annotations, the following gene is in your area of interest: HCFC1(-)
write fasta - Elapsed time since the previous call: 0.27 seconds
write fasta - Current memory usage: 172.39 MB
Length of region: 96 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: 175.96 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/16fa5ed2-95c8-449c-aae9-7c74bbdcabfd/fasta/HCFC1.fasta" "/disk1/www/rails/humanrnamap/public/result/16fa5ed2-95c8-449c-aae9-7c74bbdcabfd/ct/HCFC1.ct" --SHAPE "HCFC1.dat"

fold - Elapsed time since the previous call: 0.11 seconds
fold - Current memory usage: 175.96 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/16fa5ed2-95c8-449c-aae9-7c74bbdcabfd/ct/HCFC1.ct" "/disk1/www/rails/humanrnamap/public/result/16fa5ed2-95c8-449c-aae9-7c74bbdcabfd/fold_FE/HCFC1.txt" -sh "HCFC1.dat"

efn2 - Elapsed time since the previous call: 0.55 seconds
efn2 - Current memory usage: 175.96 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/16fa5ed2-95c8-449c-aae9-7c74bbdcabfd/ct/HCFC1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/16fa5ed2-95c8-449c-aae9-7c74bbdcabfd/fold_dbn/HCFC1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.96 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CUGGUUCUGUUUUCUUUUCUUCCCCUUGUGUUUCCAGUCACCUAACUUCCCUUCCUCAGGCUCCCCCGGCCCACCCUGCUCAGUGACCCCACAGGA', '-structureDBN', '..((.................)).((((((......(((((.................(((.......)))...........)))))..)))))).', '-o', '/disk1/www/rails/humanrnamap/public/result/16fa5ed2-95c8-449c-aae9-7c74bbdcabfd/final_image/HCFC1_fold_1.svg', '-title', 'HCFC1, -10.8 ± 1.0\n kcal/mol, AUC: 0.581', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,4,5,6,8,9,10,11,12,13,15,16,17,18,20,21,26,27,28,29,30,31,32,33,37,38,43,47,48,52,53,56,59,60,62,68,69,77,78,80,83,84,85,94,95', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '64,1,70,71,75,14,19,22,23,24,89,87,93,42,50,54,63', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '96,65,34,35,39,40,76,49,86,55,88,90,92,61', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '66,67,7,72,73,74,79,81,82,25,91,36,41,44,45,46,51,57,58']
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Text: '40', X: 166.5972301948917, Y: 161.8125550019276, Width: 18.0, Height: 8
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Text: '50', X: 216.60697993264716, Y: 8.0, Width: 18.0, Height: 8
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Text: 'HCFC1, -10.8 ± 1.0
 kcal/mol, AUC: 0.581', X: 164.18079112554068, Y: 422.76001929548795, Width: 142.5, Height: 23
Calculated bounding box: (-4.0, 0.0, 465.2873453968703, 422.76001929548795)
Updated viewBox: -9.0 -5.0 479.2873453968703 432.76001929548795
Updated SVG: /disk1/www/rails/humanrnamap/public/result/16fa5ed2-95c8-449c-aae9-7c74bbdcabfd/final_image/HCFC1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/16fa5ed2-95c8-449c-aae9-7c74bbdcabfd/final_image/HCFC1_fold_final_1.svg
