Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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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/4269a349-27b8-4bb1-bf62-9387f3d5baa7/final_image/HCFC1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.99 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.99 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.99 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.63 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: 172.63 MB
Length of region: 87 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: 0.19 seconds
write dat - Current memory usage: 176.11 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/4269a349-27b8-4bb1-bf62-9387f3d5baa7/fasta/HCFC1.fasta" "/disk1/www/rails/humanrnamap/public/result/4269a349-27b8-4bb1-bf62-9387f3d5baa7/ct/HCFC1.ct" --SHAPE "HCFC1.dat"

fold - Elapsed time since the previous call: 0.11 seconds
fold - Current memory usage: 176.11 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/4269a349-27b8-4bb1-bf62-9387f3d5baa7/ct/HCFC1.ct" "/disk1/www/rails/humanrnamap/public/result/4269a349-27b8-4bb1-bf62-9387f3d5baa7/fold_FE/HCFC1.txt" -sh "HCFC1.dat"

efn2 - Elapsed time since the previous call: 0.42 seconds
efn2 - Current memory usage: 176.11 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/4269a349-27b8-4bb1-bf62-9387f3d5baa7/ct/HCFC1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/4269a349-27b8-4bb1-bf62-9387f3d5baa7/fold_dbn/HCFC1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 176.11 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CUACUUCAAACGGGGGCACGGGCCAGCCCGAGGGUGGGCAGCAGCCCCCUGCUGGUCGCCCCUGUGAGACACACCAGACCACUUCCA', '-structureDBN', '.....((..((((((((...(((((((....(((.((((....))))))))))))))))))))))..))..................', '-o', '/disk1/www/rails/humanrnamap/public/result/4269a349-27b8-4bb1-bf62-9387f3d5baa7/final_image/HCFC1_fold_1.svg', '-title', 'HCFC1, -49.0 ± 2.1\n kcal/mol, AUC: 0.885', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,5,6,12,13,14,15,16,20,21,22,26,30,32,33,34,35,36,37,38,41,44,50,51,53,54,55,56,58,63,64,65,66,68,77,83,84', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '59,11,45,46,47,49,61,52,23,24,57,27,60,29,62', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,3,67,71,8,10,74,75,79,80,17,81,86,87,25,39,42,43,48', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '4,69,70,7,72,9,73,76,78,18,19,82,85,28,31,40']
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Text: 'HCFC1, -49.0 ± 2.1
 kcal/mol, AUC: 0.885', X: 156.25, Y: 389.5269536004991, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 454.0, 389.5269536004991)
Updated viewBox: -0.25 -5.0 459.25 399.5269536004991
Updated SVG: /disk1/www/rails/humanrnamap/public/result/4269a349-27b8-4bb1-bf62-9387f3d5baa7/final_image/HCFC1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/4269a349-27b8-4bb1-bf62-9387f3d5baa7/final_image/HCFC1_fold_final_1.svg
