Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 99% [==================================================] -                     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/e3e67f03-9e43-4690-9ab4-2b077664bee0/final_image/C9orf72_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.63 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.63 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.63 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.33 MB
Based on canonical annotations, the following gene is in your area of interest: C9orf72(-)
write fasta - Elapsed time since the previous call: 0.38 seconds
write fasta - Current memory usage: 172.33 MB
Length of region: 106 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: 175.87 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/e3e67f03-9e43-4690-9ab4-2b077664bee0/fasta/C9orf72.fasta" "/disk1/www/rails/humanrnamap/public/result/e3e67f03-9e43-4690-9ab4-2b077664bee0/ct/C9orf72.ct" --SHAPE "C9orf72.dat"

fold - Elapsed time since the previous call: 0.16 seconds
fold - Current memory usage: 175.87 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/e3e67f03-9e43-4690-9ab4-2b077664bee0/ct/C9orf72.ct" "/disk1/www/rails/humanrnamap/public/result/e3e67f03-9e43-4690-9ab4-2b077664bee0/fold_FE/C9orf72.txt" -sh "C9orf72.dat"

efn2 - Elapsed time since the previous call: 0.45 seconds
efn2 - Current memory usage: 175.87 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/e3e67f03-9e43-4690-9ab4-2b077664bee0/ct/C9orf72.ct" 1 "/disk1/www/rails/humanrnamap/public/result/e3e67f03-9e43-4690-9ab4-2b077664bee0/fold_dbn/C9orf72_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.87 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AGUGAUGGAGAAAUAACUUUUCUUGCCAACCACACUCUAAAUGGAGAAAUCCUUCGAAAUGCAGAGAGUGGUGCUAUAGAUGUAAAGUUUUUUGUCUUGUCUGAAA', '-structureDBN', '...((((((.(((.(((((((((.....(((((.((((..((...(((....)))...))..)))).))))).....)))...)))))).))).)).)))).....', '-o', '/disk1/www/rails/humanrnamap/public/result/e3e67f03-9e43-4690-9ab4-2b077664bee0/final_image/C9orf72_fold_1.svg', '-title', 'C9orf72, -23.7 ± 1.4\n kcal/mol, AUC: 0.693', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,4,6,7,8,10,14,18,19,20,21,23,24,25,36,38,42,43,44,46,50,53,54,56,60,61,64,66,68,69,70,71,72,73,75,77,79,81,82,83,87,88,89,90,91,92,93,94,95,97,98,99,100,102,103', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '32,33,35,37', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '65,9,11,12,13,76,15,85,22,27,28,29,30,31,101,39,104,41,105,106,48,49,52,55,59,63', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,67,5,74,78,16,17,80,84,86,26,96,34,40,45,47,51,57,58,62']
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Text: '50', X: -4.0, Y: 74.57414595985136, Width: 18.0, Height: 8
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Text: 'C9orf72, -23.7 ± 1.4
 kcal/mol, AUC: 0.693', X: 312.77090030488415, Y: 395.080564227976, Width: 142.5, Height: 24
Calculated bounding box: (-4.0, 5.0, 758.4788333072066, 395.080564227976)
Updated viewBox: -9.0 0.0 772.4788333072066 400.080564227976
Updated SVG: /disk1/www/rails/humanrnamap/public/result/e3e67f03-9e43-4690-9ab4-2b077664bee0/final_image/C9orf72_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/e3e67f03-9e43-4690-9ab4-2b077664bee0/final_image/C9orf72_fold_final_1.svg
