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/56531346-9871-4f06-a748-c52ab68f17de/final_image/DNAJC13_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.97 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.97 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.97 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.50 MB
Based on canonical annotations, the following gene is in your area of interest: DNAJC13(+)
write fasta - Elapsed time since the previous call: 1.20 seconds
write fasta - Current memory usage: 172.50 MB
Length of region: 104 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: 0.18 seconds
write dat - Current memory usage: 176.24 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/56531346-9871-4f06-a748-c52ab68f17de/fasta/DNAJC13.fasta" "/disk1/www/rails/humanrnamap/public/result/56531346-9871-4f06-a748-c52ab68f17de/ct/DNAJC13.ct" --SHAPE "DNAJC13.dat"

fold - Elapsed time since the previous call: 0.13 seconds
fold - Current memory usage: 176.24 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/56531346-9871-4f06-a748-c52ab68f17de/ct/DNAJC13.ct" "/disk1/www/rails/humanrnamap/public/result/56531346-9871-4f06-a748-c52ab68f17de/fold_FE/DNAJC13.txt" -sh "DNAJC13.dat"

efn2 - Elapsed time since the previous call: 0.51 seconds
efn2 - Current memory usage: 176.24 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/56531346-9871-4f06-a748-c52ab68f17de/ct/DNAJC13.ct" 1 "/disk1/www/rails/humanrnamap/public/result/56531346-9871-4f06-a748-c52ab68f17de/fold_dbn/DNAJC13_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.24 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AUGAGAGCAUUUAAUAUUGACAGAGAACUUGGAAGUGCAAAUGUGAUCUCCUGGAACCACCAUGAGUUUGAGGUUAAAUAUGAGUGCCUGGCAGAGGAAAUUAA', '-structureDBN', '..((..((((((..((((..(((.....)))..)))).))))))..)).(((.((((((...)).)))).))).............(((.....))).......', '-o', '/disk1/www/rails/humanrnamap/public/result/56531346-9871-4f06-a748-c52ab68f17de/final_image/DNAJC13_fold_1.svg', '-title', 'DNAJC13, -16.7 ± 1.2\n kcal/mol, AUC: 0.657', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,5,7,10,11,12,15,17,18,19,23,25,29,30,31,32,35,36,37,42,43,44,45,47,49,52,53,54,63,64,66,67,68,69,70,72,73,74,75,79,81,82,84,85,86,89,90,91,94,96,97,101,102', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '98,4,87,104,58,88,76', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '65,6,39,71,9,103,48,50,51,59,60', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,8,13,14,16,20,21,22,24,26,27,28,33,34,38,40,41,46,55,56,57,61,62,77,78,80,83,92,93,95,99,100']
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Text: 'DNAJC13, -16.7 ± 1.2
 kcal/mol, AUC: 0.657', X: 204.0, Y: 422.86660113301457, Width: 147.0, Height: 23
Calculated bounding box: (4.75, 5.0, 558.5, 422.86660113301457)
Updated viewBox: -0.25 0.0 563.75 427.86660113301457
Updated SVG: /disk1/www/rails/humanrnamap/public/result/56531346-9871-4f06-a748-c52ab68f17de/final_image/DNAJC13_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/56531346-9871-4f06-a748-c52ab68f17de/final_image/DNAJC13_fold_final_1.svg
