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/f951b830-e38d-4866-a44c-87e9c575d811/final_image/KPNB1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.09 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.09 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.09 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.78 MB
Based on canonical annotations, the following gene is in your area of interest: KPNB1(+)
write fasta - Elapsed time since the previous call: 0.58 seconds
write fasta - Current memory usage: 172.78 MB
Length of region: 93 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: 176.04 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/f951b830-e38d-4866-a44c-87e9c575d811/fasta/KPNB1.fasta" "/disk1/www/rails/humanrnamap/public/result/f951b830-e38d-4866-a44c-87e9c575d811/ct/KPNB1.ct" --SHAPE "KPNB1.dat"

fold - Elapsed time since the previous call: 0.10 seconds
fold - Current memory usage: 176.04 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/f951b830-e38d-4866-a44c-87e9c575d811/ct/KPNB1.ct" "/disk1/www/rails/humanrnamap/public/result/f951b830-e38d-4866-a44c-87e9c575d811/fold_FE/KPNB1.txt" -sh "KPNB1.dat"

efn2 - Elapsed time since the previous call: 0.42 seconds
efn2 - Current memory usage: 176.04 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/f951b830-e38d-4866-a44c-87e9c575d811/ct/KPNB1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/f951b830-e38d-4866-a44c-87e9c575d811/fold_dbn/KPNB1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.04 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AUCCAAUGAGAUUCUGACUGCCAUAAUCCAGGGGAUGAGGAAAGAAGAGCCUAGUAAUAAUGUGAAGCUAGCUGCUACGAAUGCACUCCUGAA', '-structureDBN', '((((..((.((((.((.....)).))))))..)))).((((.......(.(((((...........)))))).((.......))..))))...', '-o', '/disk1/www/rails/humanrnamap/public/result/f951b830-e38d-4866-a44c-87e9c575d811/final_image/KPNB1_fold_1.svg', '-title', 'KPNB1, -13.5 ± 1.0\n kcal/mol, AUC: 0.749', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,7,8,10,12,13,15,16,19,20,24,27,31,32,33,34,36,37,39,40,44,47,49,52,54,55,58,61,62,63,64,67,69,71,73,74,76,79,82,83,87,90,91', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '70,41,75,92,93', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,3,4,35,6,11,51,84,21,22,23,53', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '5,9,14,17,18,25,26,28,29,30,38,42,43,45,46,48,50,56,57,59,60,65,66,68,72,77,78,80,81,85,86,88,89']
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Text: 'KPNB1, -13.5 ± 1.0
 kcal/mol, AUC: 0.749', X: 58.56772725826926, Y: 356.7596005463196, Width: 142.5, Height: 23
Calculated bounding box: (-0.6373667793622424, 0.0, 254.88545451653852, 356.7596005463196)
Updated viewBox: -5.637366779362242 -5.0 265.52282129590077 366.7596005463196
Updated SVG: /disk1/www/rails/humanrnamap/public/result/f951b830-e38d-4866-a44c-87e9c575d811/final_image/KPNB1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/f951b830-e38d-4866-a44c-87e9c575d811/final_image/KPNB1_fold_final_1.svg
