Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 96% [================================================= ] -                     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/b0e1ecc5-a706-4912-ae8a-c154b879b844/final_image/PLEKHM2_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.60 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.60 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.60 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.12 MB
Based on canonical annotations, the following gene is in your area of interest: PLEKHM2(+)
write fasta - Elapsed time since the previous call: 1.02 seconds
write fasta - Current memory usage: 172.12 MB
Length of region: 88 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: 0.17 seconds
write dat - Current memory usage: 175.59 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/b0e1ecc5-a706-4912-ae8a-c154b879b844/fasta/PLEKHM2.fasta" "/disk1/www/rails/humanrnamap/public/result/b0e1ecc5-a706-4912-ae8a-c154b879b844/ct/PLEKHM2.ct" --SHAPE "PLEKHM2.dat"

fold - Elapsed time since the previous call: 0.10 seconds
fold - Current memory usage: 175.59 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/b0e1ecc5-a706-4912-ae8a-c154b879b844/ct/PLEKHM2.ct" "/disk1/www/rails/humanrnamap/public/result/b0e1ecc5-a706-4912-ae8a-c154b879b844/fold_FE/PLEKHM2.txt" -sh "PLEKHM2.dat"

efn2 - Elapsed time since the previous call: 0.51 seconds
efn2 - Current memory usage: 175.59 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/b0e1ecc5-a706-4912-ae8a-c154b879b844/ct/PLEKHM2.ct" 1 "/disk1/www/rails/humanrnamap/public/result/b0e1ecc5-a706-4912-ae8a-c154b879b844/fold_dbn/PLEKHM2_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.59 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CUACAGUCCACCCCUGCCCUGGGCGGCAGAACCACCGAGUGUGGCUUAAGACAGGGUCCCUCCACUCCAGGGAUCCAGAUCAGGUGCC', '-structureDBN', '........((((.(((((......)))))..((((.....)))).........((((((((.......))))))))......))))..', '-o', '/disk1/www/rails/humanrnamap/public/result/b0e1ecc5-a706-4912-ae8a-c154b879b844/final_image/PLEKHM2_fold_1.svg', '-title', 'PLEKHM2, -36.0 ± 0.8\n kcal/mol, AUC: 0.813', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,6,7,15,16,20,21,22,23,25,26,29,37,39,40,41,42,43,44,46,47,50,54,55,56,57,61,66,70,71,72,74,78,80,83,84,85,86', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '1,8,73,10,75,76,14,17,18,19,82,87,88,27,33,34,58,59,60', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '32,64,65,3,36,67,68,69,9,11,12,49,81,51,28', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '4,5,13,77,79,24,30,31,35,38,45,48,52,53,62,63']
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Text: 'PLEKHM2, -36.0 ± 0.8
 kcal/mol, AUC: 0.813', X: 150.81096473014725, Y: 301.95246486150563, Width: 148.5, Height: 23
Calculated bounding box: (4.75, 5.0, 445.3719294602945, 301.95246486150563)
Updated viewBox: -0.25 0.0 450.6219294602945 306.95246486150563
Updated SVG: /disk1/www/rails/humanrnamap/public/result/b0e1ecc5-a706-4912-ae8a-c154b879b844/final_image/PLEKHM2_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/b0e1ecc5-a706-4912-ae8a-c154b879b844/final_image/PLEKHM2_fold_final_1.svg
