Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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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/b0a04808-46ad-4a3e-a939-6222b1aa840a/final_image/TGOLN2_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 157.63 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 157.63 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 157.63 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 171.23 MB
Based on canonical annotations, the following gene is in your area of interest: TGOLN2(-)
write fasta - Elapsed time since the previous call: 0.76 seconds
write fasta - Current memory usage: 171.23 MB
Length of region: 101 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: 174.61 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/b0a04808-46ad-4a3e-a939-6222b1aa840a/fasta/TGOLN2.fasta" "/disk1/www/rails/humanrnamap/public/result/b0a04808-46ad-4a3e-a939-6222b1aa840a/ct/TGOLN2.ct" --SHAPE "TGOLN2.dat"

fold - Elapsed time since the previous call: 0.10 seconds
fold - Current memory usage: 174.61 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/b0a04808-46ad-4a3e-a939-6222b1aa840a/ct/TGOLN2.ct" "/disk1/www/rails/humanrnamap/public/result/b0a04808-46ad-4a3e-a939-6222b1aa840a/fold_FE/TGOLN2.txt" -sh "TGOLN2.dat"

efn2 - Elapsed time since the previous call: 0.44 seconds
efn2 - Current memory usage: 174.61 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/b0a04808-46ad-4a3e-a939-6222b1aa840a/ct/TGOLN2.ct" 1 "/disk1/www/rails/humanrnamap/public/result/b0a04808-46ad-4a3e-a939-6222b1aa840a/fold_dbn/TGOLN2_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 174.61 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CCUUUUCCCUUCCUUUCCCCUCCUCAUGUUUUCUGGUUGUGCCCAUCUGUACCAGCUCCUUUCCAUCCACCUUCGUAUGCACCCAGAUUUUUCUGUUCCCA', '-structureDBN', '...............................(((((..((((......((((......................)))))))))))))..............', '-o', '/disk1/www/rails/humanrnamap/public/result/b0a04808-46ad-4a3e-a939-6222b1aa840a/final_image/TGOLN2_fold_1.svg', '-title', 'TGOLN2, -11.3 ± 1.1\n kcal/mol, AUC: 0.542', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,4,5,6,10,11,14,15,16,21,24,27,28,29,30,31,32,34,35,36,37,38,39,40,41,46,48,49,50,55,57,60,61,62,66,72,73,75,76,78,79,86,88,89,90,91,92,94,95,96,97', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '64,1,2,69,7,8,12,13,17,18,81,82,83,22,23,87,93,33,98,99,42,59', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '65,67,71,80,19,85,26,101,43,45,47,51,52,53,54,58,63', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '68,100,70,9,74,44,77,20,84,56,25']
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Text: 'TGOLN2, -11.3 ± 1.1
 kcal/mol, AUC: 0.542', X: 348.75, Y: 248.63038041670265, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 851.9901511824944, 248.63038041670265)
Updated viewBox: -0.25 0.0 857.2401511824944 253.63038041670265
Updated SVG: /disk1/www/rails/humanrnamap/public/result/b0a04808-46ad-4a3e-a939-6222b1aa840a/final_image/TGOLN2_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/b0a04808-46ad-4a3e-a939-6222b1aa840a/final_image/TGOLN2_fold_final_1.svg
