Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
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 97% [================================================= ] \                     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/c1ec7c0b-45cb-4e26-8034-163709462bb7/final_image/HCFC1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.05 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.05 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.05 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.61 MB
Based on canonical annotations, the following gene is in your area of interest: HCFC1(-)
write fasta - Elapsed time since the previous call: 0.26 seconds
write fasta - Current memory usage: 172.61 MB
Length of region: 72 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: 175.97 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/c1ec7c0b-45cb-4e26-8034-163709462bb7/fasta/HCFC1.fasta" "/disk1/www/rails/humanrnamap/public/result/c1ec7c0b-45cb-4e26-8034-163709462bb7/ct/HCFC1.ct" --SHAPE "HCFC1.dat"

fold - Elapsed time since the previous call: 0.09 seconds
fold - Current memory usage: 175.97 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/c1ec7c0b-45cb-4e26-8034-163709462bb7/ct/HCFC1.ct" "/disk1/www/rails/humanrnamap/public/result/c1ec7c0b-45cb-4e26-8034-163709462bb7/fold_FE/HCFC1.txt" -sh "HCFC1.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 175.97 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/c1ec7c0b-45cb-4e26-8034-163709462bb7/ct/HCFC1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/c1ec7c0b-45cb-4e26-8034-163709462bb7/fold_dbn/HCFC1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.97 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CCCUGCUUCAGGAACACCCGCCAGGGCCCACCCCUCCCACCCCGUCCCAGCAUUCGCACUUCACCCUCGCGA', '-structureDBN', '...((((...(((.........((((.....)))).........))).)))).((((...........))))', '-o', '/disk1/www/rails/humanrnamap/public/result/c1ec7c0b-45cb-4e26-8034-163709462bb7/final_image/HCFC1_fold_1.svg', '-title', 'HCFC1, -15.1 ± 0.8\n kcal/mol, AUC: 0.566', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '67,4,5,69,7,8,71,11,12,20,24,25,26,35,44,45,50,53,54,56,60,61', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '32,65,3,36,37,72,41,46,18,22,57', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,2,66,70,9,10,14,15,16,17,21,23,30,33,40,42,47,48,49,51,55,63', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,68,6,13,19,27,28,29,31,34,38,39,43,52,58,59,62']
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Text: 'HCFC1, -15.1 ± 0.8
 kcal/mol, AUC: 0.566', X: 63.79276040437384, Y: 366.7033514274827, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 288.85592419465183, 366.7033514274827)
Updated viewBox: -0.25 0.0 294.10592419465183 371.7033514274827
Updated SVG: /disk1/www/rails/humanrnamap/public/result/c1ec7c0b-45cb-4e26-8034-163709462bb7/final_image/HCFC1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/c1ec7c0b-45cb-4e26-8034-163709462bb7/final_image/HCFC1_fold_final_1.svg
