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/82df30c3-1529-4291-8696-6d698095ccdd/final_image/HCFC1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.12 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.12 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.12 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.79 MB
Based on canonical annotations, the following gene is in your area of interest: HCFC1(-)
write fasta - Elapsed time since the previous call: 0.25 seconds
write fasta - Current memory usage: 172.79 MB
Length of region: 81 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: 176.21 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/82df30c3-1529-4291-8696-6d698095ccdd/fasta/HCFC1.fasta" "/disk1/www/rails/humanrnamap/public/result/82df30c3-1529-4291-8696-6d698095ccdd/ct/HCFC1.ct" --SHAPE "HCFC1.dat"

fold - Elapsed time since the previous call: 0.10 seconds
fold - Current memory usage: 176.21 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/82df30c3-1529-4291-8696-6d698095ccdd/ct/HCFC1.ct" "/disk1/www/rails/humanrnamap/public/result/82df30c3-1529-4291-8696-6d698095ccdd/fold_FE/HCFC1.txt" -sh "HCFC1.dat"

efn2 - Elapsed time since the previous call: 0.51 seconds
efn2 - Current memory usage: 176.21 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/82df30c3-1529-4291-8696-6d698095ccdd/ct/HCFC1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/82df30c3-1529-4291-8696-6d698095ccdd/fold_dbn/HCFC1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 176.21 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CCUGGUGCAGCAGCAGCAGCUGCAGGAGGCCCAGGCCCAGCAGCAGCAUCACCACCUCCCCACUGAGGCCCUGGCCCCUGC', '-structureDBN', '.(((.(((....))).)))..(((((.((((.((((((((......................))).))).)))))))))))', '-o', '/disk1/www/rails/humanrnamap/public/result/82df30c3-1529-4291-8696-6d698095ccdd/final_image/HCFC1_fold_1.svg', '-title', 'HCFC1, -35.1 ± 0.9\n kcal/mol, AUC: 0.667', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '64,65,3,4,5,6,7,67,68,10,72,73,13,74,79,16,80,19,21,22,25,26,28,29,34,35,40,43,46,49,57', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '1,36,75,76,77,14,78,81,20,31', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '2,37,8,9,42,11,12,44,47,17,23,56,30', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '66,69,70,71,15,18,24,27,32,33,38,39,41,45,48,50,51,52,53,54,55,58,59,60,61,62,63']
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Text: 'HCFC1, -35.1 ± 0.9
 kcal/mol, AUC: 0.667', X: 77.91679298538452, Y: 507.0019528752218, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 303.0435505789199, 507.0019528752218)
Updated viewBox: -0.25 -5.0 308.2935505789199 517.0019528752218
Updated SVG: /disk1/www/rails/humanrnamap/public/result/82df30c3-1529-4291-8696-6d698095ccdd/final_image/HCFC1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/82df30c3-1529-4291-8696-6d698095ccdd/final_image/HCFC1_fold_final_1.svg
